| Title: | Companion package to chipenrich |
|---|---|
| Description: | Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. |
| Authors: | Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Laura J. Scott [ths], Maureen A. Sartor [ths] |
| Maintainer: | Kai Wang <[email protected]> |
| License: | GPL-3 |
| Version: | 2.36.0 |
| Built: | 2026-10-10 11:17:24 UTC |
| Source: | https://github.com/bioc/chipenrich.data |
Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates.
A GRanges with all the enhancer locations for hg19. The locations were found using a combination of DNAse data and from Thurman et al (PMID: 22955617)
enhancer.dnase_thurman.0enhancer.dnase_thurman.0
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
A data frame with gene-level descriptions of enhancer properties using enhancers.dnase_thurman.0. Used in the adjustment of proximity test to enhancers.
The Entrez ID for the a gene
The empirical average distance to an enhancer from 90 ENCODE ChIP-seq datasets. This is used as the adjustment.
The number of enhancers assigned to the gene, defined by closest gene TSS
The theoretical average distance to an enhancer assuming every base pair on the genome is equally likely to have a peak binding.
gene.enh.descgene.enh.desc
An object of class data.frame with 21600 rows and 4 columns.
"GeneSet"
Class for storing sets of genes and their corresponding metadata.
Objects can be created by calls of the form new("GeneSet").
These objects are used internally by the chipenrich package and users will not likely need to create these.
set.gene:Object of class "environment". Maps from geneset IDs to lists of Entrez gene IDs.
type:Object of class "character". The formal name for this collection of genesets.
set.name:Object of class "environment". Maps from geneset IDs to their descriptions/names.
all.genes:Object of class "character". A set of all genes present across every geneset.
organism:Object of class "character". Organism code for gene IDs.
dburl:Object of class "character". Web URL for this collection of genesets.
Not typically accessed by the user - this is used internally by the chipenrich package.
Ryan Welch [email protected]
# Show information about class. showClass("GeneSet") # What is stored inside a geneset object? data("geneset.metabolite.hsa"); str(geneset.metabolite.hsa); # How are the mappings from geneset IDs to gene IDs stored? ls.str([email protected]);# Show information about class. showClass("GeneSet") # What is stored inside a geneset object? data("geneset.metabolite.hsa"); str(geneset.metabolite.hsa); # How are the mappings from geneset IDs to gene IDs stored? ls.str(geneset.metabolite.hsa@set.gene);
BioCarta (biocarta_pathway) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:04 2017.
geneset.biocarta_pathway.hsageneset.biocarta_pathway.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.biocarta_pathway.mmu)data(geneset.biocarta_pathway.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.biocarta_pathway.rno)data(geneset.biocarta_pathway.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
Comparative Toxicogenomics Database (ctd) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:11 2017.
geneset.ctd.hsageneset.ctd.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://ctdbase.org
Comparative Toxicogenomics Database (ctd) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Sat Nov 10 15:56:37 2018.
geneset.ctd.mmugeneset.ctd.mmu
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://ctdbase.org
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.cytoband.hsa)data(geneset.cytoband.hsa)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
DrugBank (drug_bank) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:13 2017.
geneset.drug_bank.hsageneset.drug_bank.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
https://www.drugbank.ca
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.drug_bank.mmu)data(geneset.drug_bank.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.drug_bank.rno)data(geneset.drug_bank.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
Gene Ontology Biological Process (GOBP) genesets for Drosophila melanogaster. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:38 2017.
geneset.GOBP.dmegeneset.GOBP.dme
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Biological Process (GOBP) genesets for Danio rerio. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:25:08 2017.
geneset.GOBP.dregeneset.GOBP.dre
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dr.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Biological Process (GOBP) genesets for Homo sapiens. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:22:22 2017.
geneset.GOBP.hsageneset.GOBP.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Hs.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Biological Process (GOBP) genesets for Mus musculus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:23:23 2017.
geneset.GOBP.mmugeneset.GOBP.mmu
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Mm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Biological Process (GOBP) genesets for Rattus norvegicus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:10 2017.
geneset.GOBP.rnogeneset.GOBP.rno
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Rn.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Cellular Component (GOCC) genesets for Drosophila melanogaster. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:38 2017.
geneset.GOCC.dmegeneset.GOCC.dme
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Cellular Component (GOCC) genesets for Danio rerio. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:25:08 2017.
geneset.GOCC.dregeneset.GOCC.dre
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dr.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Cellular Component (GOCC) genesets for Homo sapiens. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:22:22 2017.
geneset.GOCC.hsageneset.GOCC.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Hs.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Cellular Component (GOCC) genesets for Mus musculus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:23:23 2017.
geneset.GOCC.mmugeneset.GOCC.mmu
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Mm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Cellular Component (GOCC) genesets for Rattus norvegicus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:10 2017.
geneset.GOCC.rnogeneset.GOCC.rno
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Rn.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Molecular Function (GOMF) genesets for Drosophila melanogaster. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:38 2017.
geneset.GOMF.dmegeneset.GOMF.dme
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Molecular Function (GOMF) genesets for Danio rerio. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:25:08 2017.
geneset.GOMF.dregeneset.GOMF.dre
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Dr.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Molecular Function (GOMF) genesets for Homo sapiens. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:22:22 2017.
geneset.GOMF.hsageneset.GOMF.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Hs.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Molecular Function (GOMF) genesets for Mus musculus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:23:23 2017.
geneset.GOMF.mmugeneset.GOMF.mmu
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Mm.eg.db_3.4.2 and GO.db_3.4.2
Gene Ontology Molecular Function (GOMF) genesets for Rattus norvegicus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 16:24:10 2017.
geneset.GOMF.rnogeneset.GOMF.rno
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
org.Rn.eg.db_3.4.2 and GO.db_3.4.2
Hallmark (MSigDB) (hallmark) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:15 2017.
geneset.hallmark.hsageneset.hallmark.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://software.broadinstitute.org/gsea/msigdb/collections.jsp#H
Immunologic Signatures (MSigDB) (immunologic) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:45 2017.
geneset.immunologic.hsageneset.immunologic.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C7
KEGG Pathways (kegg_pathway) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:53 2017.
geneset.kegg_pathway.hsageneset.kegg_pathway.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://kegg.jp
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.kegg_pathway.mmu)data(geneset.kegg_pathway.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.kegg_pathway.rno)data(geneset.kegg_pathway.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.mesh.hsa)data(geneset.mesh.hsa)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.mesh.mmu)data(geneset.mesh.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.mesh.rno)data(geneset.mesh.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.metabolite.hsa)data(geneset.metabolite.hsa)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.metabolite.mmu)data(geneset.metabolite.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.metabolite.rno)data(geneset.metabolite.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
MicroRNA Targets (MSigDB) (microrna) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:46:56 2017.
geneset.microrna.hsageneset.microrna.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C3
Oncogenic Signatures (MSigDB) (oncogenic) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:47:23 2017.
geneset.oncogenic.hsageneset.oncogenic.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C6
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.panther_pathway.hsa)data(geneset.panther_pathway.hsa)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.panther_pathway.mmu)data(geneset.panther_pathway.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.panther_pathway.rno)data(geneset.panther_pathway.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
Pfam (pfam) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:47:28 2017.
geneset.pfam.hsageneset.pfam.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://pfam.xfam.org
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.pfam.mmu)data(geneset.pfam.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.pfam.rno)data(geneset.pfam.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
BioGRID Protein Interactions (protein_interaction_biogrid) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Tue Oct 24 16:05:53 2017.
geneset.protein_interaction_biogrid.hsageneset.protein_interaction_biogrid.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
https://thebiogrid.org
Reactome genesets for Drosophila melanogaster. All genesets are required to have >= 10 Entrez IDs. Built on Mon Mar 20 15:14:03 2017.
geneset.reactome.dmegeneset.reactome.dme
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. Reactome.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. R-HSA-109688), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://www.reactome.org/download/current/NCBI2Reactome_All_Levels.txt downloaded on 2017-03-19
Reactome genesets for Danio rerio. All genesets are required to have >= 10 Entrez IDs. Built on Tue Mar 28 13:03:21 2017.
geneset.reactome.dregeneset.reactome.dre
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. Reactome.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. R-HSA-109688), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://www.reactome.org/download/current/NCBI2Reactome_All_Levels.txt downloaded on 2017-03-19
Reactome genesets for Homo sapiens. All genesets are required to have >= 10 Entrez IDs. Built on Mon Mar 20 15:13:45 2017.
geneset.reactome.hsageneset.reactome.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. Reactome.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. R-HSA-109688), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://www.reactome.org/download/current/NCBI2Reactome_All_Levels.txt downloaded on 2017-03-19
Reactome genesets for Mus musculus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Mar 20 15:13:55 2017.
geneset.reactome.mmugeneset.reactome.mmu
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. Reactome.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. R-HSA-109688), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://www.reactome.org/download/current/NCBI2Reactome_All_Levels.txt downloaded on 2017-03-19
Reactome genesets for Rattus norvegicus. All genesets are required to have >= 10 Entrez IDs. Built on Mon Mar 20 15:13:59 2017.
geneset.reactome.rnogeneset.reactome.rno
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. Reactome.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. R-HSA-109688), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://www.reactome.org/download/current/NCBI2Reactome_All_Levels.txt downloaded on 2017-03-19
Transcription Factor Targets (MSigDB) (transcription_factors) genesets. All genesets are required to have >= 10 Entrez IDs. Built on Mon Oct 16 18:47:33 2017.
geneset.transcription_factors.hsageneset.transcription_factors.hsa
A GeneSet object with the following slots:
A character indicating the type of genesets, e.g. GOBP.
A character of the URL of the database underlying the genesets.
A character of the organism, e.g. Homo sapiens.
An environment containing a list whose keys are database specific accessions (e.g. GO IDs for GO terms), and whose elements are character vectors of Entrez Gene IDs.
A character vector of all the Entrez Gene IDs contained over all the genesets in this type.
An environment containing a list whose keys are database specific accessions, and whose elements are human readable geneset names.
http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C3
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.transcription_factors.mmu)data(geneset.transcription_factors.mmu)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
GeneSet object which stores information about sets of genes.
These objects are used internally by the chipenrich package.
data(geneset.transcription_factors.rno)data(geneset.transcription_factors.rno)
See GeneSet-class for a description of the format.
For more information about genesets: chipenrich.data
For information regarding how the genesets were created: browseVignettes("chipenrich.data")
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.danRer10.10kblocusdef.danRer10.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:27 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.danRer10.10kb_outsidelocusdef.danRer10.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:27 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.danRer10.10kb_outside_upstreamlocusdef.danRer10.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:27 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.danRer10.1kblocusdef.danRer10.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:25 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.danRer10.1kb_outsidelocusdef.danRer10.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:26 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.danRer10.1kb_outside_upstreamlocusdef.danRer10.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:25 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.danRer10.5kblocusdef.danRer10.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:26 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.danRer10.5kb_outsidelocusdef.danRer10.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:27 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.danRer10.5kb_outside_upstreamlocusdef.danRer10.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:26 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.danRer10.exonlocusdef.danRer10.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:24 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.danRer10.intronlocusdef.danRer10.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:25 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.danRer10.nearest_genelocusdef.danRer10.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:23 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.danRer10.nearest_tsslocusdef.danRer10.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, danRer10.
A character indicating the organism name. In this case, Danio rerio.
Built on Fri Apr 13 09:54:22 2018.
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.dm3.10kblocusdef.dm3.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm3.10kb_outsidelocusdef.dm3.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:06 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm3.10kb_outside_upstreamlocusdef.dm3.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.dm3.1kblocusdef.dm3.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm3.1kb_outsidelocusdef.dm3.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm3.1kb_outside_upstreamlocusdef.dm3.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.dm3.5kblocusdef.dm3.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm3.5kb_outsidelocusdef.dm3.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm3.5kb_outside_upstreamlocusdef.dm3.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:05 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.dm3.exonlocusdef.dm3.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:04 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.dm3.intronlocusdef.dm3.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:04 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.dm3.nearest_genelocusdef.dm3.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:03 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.dm3.nearest_tsslocusdef.dm3.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm3.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm3 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:03 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.dm6.10kblocusdef.dm6.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm6.10kb_outsidelocusdef.dm6.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm6.10kb_outside_upstreamlocusdef.dm6.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.dm6.1kblocusdef.dm6.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:34 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm6.1kb_outsidelocusdef.dm6.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm6.1kb_outside_upstreamlocusdef.dm6.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:34 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.dm6.5kblocusdef.dm6.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.dm6.5kb_outsidelocusdef.dm6.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.dm6.5kb_outside_upstreamlocusdef.dm6.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:35 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.dm6.exonlocusdef.dm6.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:33 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.dm6.intronlocusdef.dm6.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:34 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.dm6.nearest_genelocusdef.dm6.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:33 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.dm6.nearest_tsslocusdef.dm6.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, dm6.
A character indicating the organism name. In this case, Drosophila melanogaster.
For the dm6 genome, original gene IDs are from FLYBASE and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:53:33 2018.
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.hg19.10kblocusdef.hg19.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:58 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg19.10kb_outsidelocusdef.hg19.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:59 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg19.10kb_outside_upstreamlocusdef.hg19.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:58 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.hg19.1kblocusdef.hg19.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:55 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg19.1kb_outsidelocusdef.hg19.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:56 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg19.1kb_outside_upstreamlocusdef.hg19.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:56 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.hg19.5kblocusdef.hg19.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:57 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg19.5kb_outsidelocusdef.hg19.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:58 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg19.5kb_outside_upstreamlocusdef.hg19.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:57 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.hg19.exonlocusdef.hg19.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:53 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.hg19.intronlocusdef.hg19.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:55 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.hg19.nearest_genelocusdef.hg19.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:51 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.hg19.nearest_tsslocusdef.hg19.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg19.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:45:51 2018.
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.hg38.10kblocusdef.hg38.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:42 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg38.10kb_outsidelocusdef.hg38.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:43 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg38.10kb_outside_upstreamlocusdef.hg38.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:43 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.hg38.1kblocusdef.hg38.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:39 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg38.1kb_outsidelocusdef.hg38.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:40 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg38.1kb_outside_upstreamlocusdef.hg38.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:39 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.hg38.5kblocusdef.hg38.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:41 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.hg38.5kb_outsidelocusdef.hg38.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:42 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.hg38.5kb_outside_upstreamlocusdef.hg38.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:41 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.hg38.exonlocusdef.hg38.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:37 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.hg38.intronlocusdef.hg38.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:38 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.hg38.nearest_genelocusdef.hg38.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:34 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.hg38.nearest_tsslocusdef.hg38.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, hg38.
A character indicating the organism name. In this case, Homo sapiens.
Built on Fri Apr 13 09:49:34 2018.
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.mm10.10kblocusdef.mm10.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:40 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm10.10kb_outsidelocusdef.mm10.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:41 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm10.10kb_outside_upstreamlocusdef.mm10.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:40 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.mm10.1kblocusdef.mm10.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:37 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm10.1kb_outsidelocusdef.mm10.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:38 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm10.1kb_outside_upstreamlocusdef.mm10.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:37 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.mm10.5kblocusdef.mm10.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:38 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm10.5kb_outsidelocusdef.mm10.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:39 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm10.5kb_outside_upstreamlocusdef.mm10.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:39 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.mm10.exonlocusdef.mm10.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:35 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.mm10.intronlocusdef.mm10.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:36 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.mm10.nearest_genelocusdef.mm10.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:33 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.mm10.nearest_tsslocusdef.mm10.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm10.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:51:33 2018.
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.mm9.10kblocusdef.mm9.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:44 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm9.10kb_outsidelocusdef.mm9.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:44 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm9.10kb_outside_upstreamlocusdef.mm9.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:44 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.mm9.1kblocusdef.mm9.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:41 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm9.1kb_outsidelocusdef.mm9.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:42 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm9.1kb_outside_upstreamlocusdef.mm9.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:41 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.mm9.5kblocusdef.mm9.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:42 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.mm9.5kb_outsidelocusdef.mm9.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:43 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.mm9.5kb_outside_upstreamlocusdef.mm9.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:43 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.mm9.exonlocusdef.mm9.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:39 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.mm9.intronlocusdef.mm9.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:41 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.mm9.nearest_genelocusdef.mm9.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:37 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.mm9.nearest_tsslocusdef.mm9.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, mm9.
A character indicating the organism name. In this case, Mus musculus.
Built on Fri Apr 13 09:50:37 2018.
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.rn4.10kblocusdef.rn4.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:02 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn4.10kb_outsidelocusdef.rn4.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:03 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn4.10kb_outside_upstreamlocusdef.rn4.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:02 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.rn4.1kblocusdef.rn4.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:01 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn4.1kb_outsidelocusdef.rn4.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:01 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn4.1kb_outside_upstreamlocusdef.rn4.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:01 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.rn4.5kblocusdef.rn4.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:01 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn4.5kb_outsidelocusdef.rn4.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:02 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn4.5kb_outside_upstreamlocusdef.rn4.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:02 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.rn4.exonlocusdef.rn4.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:51:59 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.rn4.intronlocusdef.rn4.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:52:00 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.rn4.nearest_genelocusdef.rn4.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:51:58 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.rn4.nearest_tsslocusdef.rn4.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn4.
A character indicating the organism name. In this case, Rattus norvegicus.
For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.
Built on Fri Apr 13 09:51:58 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.rn5.10kblocusdef.rn5.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:20 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn5.10kb_outsidelocusdef.rn5.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:21 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn5.10kb_outside_upstreamlocusdef.rn5.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:21 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.rn5.1kblocusdef.rn5.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:19 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn5.1kb_outsidelocusdef.rn5.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:19 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn5.1kb_outside_upstreamlocusdef.rn5.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:19 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.rn5.5kblocusdef.rn5.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:20 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn5.5kb_outsidelocusdef.rn5.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:20 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn5.5kb_outside_upstreamlocusdef.rn5.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:20 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.rn5.exonlocusdef.rn5.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:17 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.rn5.intronlocusdef.rn5.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:19 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.rn5.nearest_genelocusdef.rn5.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:16 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.rn5.nearest_tsslocusdef.rn5.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn5.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:16 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 10kb upstream and downstream of the TSS.
locusdef.rn6.10kblocusdef.rn6.10kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:39 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn6.10kb_outsidelocusdef.rn6.10kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:40 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 10kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn6.10kb_outside_upstreamlocusdef.rn6.10kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:39 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 1kb upstream and downstream of the TSS.
locusdef.rn6.1kblocusdef.rn6.1kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:38 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn6.1kb_outsidelocusdef.rn6.1kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:38 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn6.1kb_outside_upstreamlocusdef.rn6.1kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:38 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined within 5kb upstream and downstream of the TSS.
locusdef.rn6.5kblocusdef.rn6.5kb
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:38 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream and downstream of the TSS and bounded by the midpoints between the TSS and the next upstream and downstream TSSs.
locusdef.rn6.5kb_outsidelocusdef.rn6.5kb_outside
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:39 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.
locusdef.rn6.5kb_outside_upstreamlocusdef.rn6.5kb_outside_upstream
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:39 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the exons belonging to genes.
locusdef.rn6.exonlocusdef.rn6.exon
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:36 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the introns belonging to genes.
locusdef.rn6.intronlocusdef.rn6.intron
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:37 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.
locusdef.rn6.nearest_genelocusdef.rn6.nearest_gene
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:35 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs.
locusdef.rn6.nearest_tsslocusdef.rn6.nearest_tss
A LocusDefinition object with the following slots:
A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol
A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol
A character indicating the genome build. In this case, rn6.
A character indicating the organism name. In this case, Rattus norvegicus.
Built on Fri Apr 13 09:52:34 2018.
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.
"LocusDefinition"
A storage class representing gene locus definitions and their corresponding metadata.
Objects can be created by calls of the form new("LocusDefinition").
These objects are used internally by the chipenrich package and users will not likely need to create these.
dframe:Object of class "data.frame". Each row represents a locus for a particular geneid.
granges:Object of class "GenomicRanges". Locus definitions stored as a GenomicRanges object.
genome.build:Object of class "character". Genome build these definitions were generated from.
organism:Object of class "character". Organism code.
Not typically accessed by the user - this is used internally by the chipenrich package.
Ryan Welch [email protected]
# Show info about the class. showClass("LocusDefinition"); # Example of what a locus definition object looks like. data(locusdef.mm9.nearest_tss) lapply(attributes(locusdef.mm9.nearest_tss), head)# Show info about the class. showClass("LocusDefinition"); # Example of what a locus definition object looks like. data(locusdef.mm9.nearest_tss) lapply(attributes(locusdef.mm9.nearest_tss), head)
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.100mer)data(mappa.hg19.10kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.24mer)data(mappa.hg19.10kb.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.36mer)data(mappa.hg19.10kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.40mer)data(mappa.hg19.10kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.50mer)data(mappa.hg19.10kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 10kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.10kb.75mer)data(mappa.hg19.10kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.100mer)data(mappa.hg19.1kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.24mer)data(mappa.hg19.1kb.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.36mer)data(mappa.hg19.1kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.40mer)data(mappa.hg19.1kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.50mer)data(mappa.hg19.1kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 1kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.1kb.75mer)data(mappa.hg19.1kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.100mer)data(mappa.hg19.5kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.24mer)data(mappa.hg19.5kb.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.36mer)data(mappa.hg19.5kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.40mer)data(mappa.hg19.5kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.50mer)data(mappa.hg19.5kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: 5kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.5kb.75mer)data(mappa.hg19.5kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.100mer)data(mappa.hg19.exon.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.24mer)data(mappa.hg19.exon.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.36mer)data(mappa.hg19.exon.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.40mer)data(mappa.hg19.exon.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.50mer)data(mappa.hg19.exon.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: exon
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.exon.75mer)data(mappa.hg19.exon.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.100mer)data(mappa.hg19.intron.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.24mer)data(mappa.hg19.intron.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.36mer)data(mappa.hg19.intron.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.40mer)data(mappa.hg19.intron.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.50mer)data(mappa.hg19.intron.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: intron
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.intron.75mer)data(mappa.hg19.intron.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.100mer)data(mappa.hg19.nearest_gene.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.24mer)data(mappa.hg19.nearest_gene.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.36mer)data(mappa.hg19.nearest_gene.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.40mer)data(mappa.hg19.nearest_gene.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.50mer)data(mappa.hg19.nearest_gene.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_gene
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_gene.75mer)data(mappa.hg19.nearest_gene.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.100mer)data(mappa.hg19.nearest_tss.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 24mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.24mer)data(mappa.hg19.nearest_tss.24mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.36mer)data(mappa.hg19.nearest_tss.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.40mer)data(mappa.hg19.nearest_tss.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.50mer)data(mappa.hg19.nearest_tss.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: hg19
Locus definition: nearest_tss
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.hg19.nearest_tss.75mer)data(mappa.hg19.nearest_tss.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 10kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.10kb.100mer)data(mappa.mm9.10kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 10kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.10kb.36mer)data(mappa.mm9.10kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 10kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.10kb.40mer)data(mappa.mm9.10kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 10kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.10kb.50mer)data(mappa.mm9.10kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 10kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.10kb.75mer)data(mappa.mm9.10kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 1kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.1kb.100mer)data(mappa.mm9.1kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 1kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.1kb.36mer)data(mappa.mm9.1kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 1kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.1kb.40mer)data(mappa.mm9.1kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 1kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.1kb.50mer)data(mappa.mm9.1kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 1kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.1kb.75mer)data(mappa.mm9.1kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 5kb
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.5kb.100mer)data(mappa.mm9.5kb.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 5kb
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.5kb.36mer)data(mappa.mm9.5kb.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 5kb
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.5kb.40mer)data(mappa.mm9.5kb.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 5kb
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.5kb.50mer)data(mappa.mm9.5kb.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: 5kb
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.5kb.75mer)data(mappa.mm9.5kb.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: exon
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.exon.100mer)data(mappa.mm9.exon.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: exon
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.exon.36mer)data(mappa.mm9.exon.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: exon
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.exon.40mer)data(mappa.mm9.exon.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: exon
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.exon.50mer)data(mappa.mm9.exon.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: exon
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.exon.75mer)data(mappa.mm9.exon.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: intron
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.intron.100mer)data(mappa.mm9.intron.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: intron
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.intron.36mer)data(mappa.mm9.intron.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: intron
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.intron.40mer)data(mappa.mm9.intron.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: intron
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.intron.50mer)data(mappa.mm9.intron.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: intron
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.intron.75mer)data(mappa.mm9.intron.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_gene
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_gene.100mer)data(mappa.mm9.nearest_gene.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_gene
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_gene.36mer)data(mappa.mm9.nearest_gene.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_gene
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_gene.40mer)data(mappa.mm9.nearest_gene.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_gene
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_gene.50mer)data(mappa.mm9.nearest_gene.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_gene
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_gene.75mer)data(mappa.mm9.nearest_gene.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_tss
K-Mer Reads: 100mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_tss.100mer)data(mappa.mm9.nearest_tss.100mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_tss
K-Mer Reads: 36mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_tss.36mer)data(mappa.mm9.nearest_tss.36mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_tss
K-Mer Reads: 40mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_tss.40mer)data(mappa.mm9.nearest_tss.40mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_tss
K-Mer Reads: 50mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_tss.50mer)data(mappa.mm9.nearest_tss.50mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
Gene locus mappability data, calculated for:
Build: mm9
Locus definition: nearest_tss
K-Mer Reads: 75mer
These objects are used internally by the chipenrich package.
data(mappa.mm9.nearest_tss.75mer)data(mappa.mm9.nearest_tss.75mer)
A data frame containing:
geneidEntrez Gene IDs
mappaGene locus mappability
Ryan Welch [email protected]
For more information about gene locus definitions: chipenrich.data
A dataset containing the binding locations (peaks) of the transcription factor E2F4 called from a ChIP-seq experiment
peaks_E2F4peaks_E2F4
A data frame containing 16,245 peak binding locations. Each row is a peak location, and the 3 variables/columns are chromosome, start peak coordinate, and end peak coordinate. Peak coordinates are in hg19 (UCSC) coordinates.
The data and information regarding the experiment can be found in the following publication:
Lee, B. K., A. A. Bhinge, et al. (2011). "Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis." Nucleic Acids Res 39(9): 3558-3573.
# Load E2F4 peak data. data(peaks_E2F4) # Print the first 10 peaks in the dataset. print(head(peaks_E2F4))# Load E2F4 peak data. data(peaks_E2F4) # Print the first 10 peaks in the dataset. print(head(peaks_E2F4))
A dataset containing the binding locations (peaks) of the histone modification H3K4me3 called from a ChIP-seq experiment in the GM12878 cell line
peaks_H3K4me3_GM12878peaks_H3K4me3_GM12878
A data frame containing 57,476 peak binding locations. Each row is a peak location, and the 3 variables/columns are chromosome, start peak coordinate, and end peak coordinate. Peak coordinates are in hg19 (UCSC) coordinates.
The data and information regarding the experiment can be found at the following ENCODE URL:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me3StdPkV2.broadPeak.gz
# Load H3K4me3 in GM12878 peak data. data(peaks_H3K4me3_GM12878) # Print the first 10 peaks in the dataset. print(head(peaks_H3K4me3_GM12878))# Load H3K4me3 in GM12878 peak data. data(peaks_H3K4me3_GM12878) # Print the first 10 peaks in the dataset. print(head(peaks_H3K4me3_GM12878))
A mgcv::gam object on a combined data of 90 ENCODE ChIP-seq datasets that modeled the relationship between a gene's locus length the distance from a peak to the gene's transcription start site, using a cubic spline. This is used to adjust for the proximity to TSSes test.
spline.log_dtss.90ENCODEspline.log_dtss.90ENCODE
An object of class gam (inherits from glm, lm) of length 46.
A GRanges with all the TSSs for danRer10. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.danRer10tss.danRer10
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Drerio.UCSC.danRer10.refGene_3.4.2 and org.Dr.eg.db_3.5.0.
A GRanges with all the TSSs for dm3. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.dm3tss.dm3
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 and org.Dm.eg.db_3.5.0.
A GRanges with all the TSSs for dm6. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.dm6tss.dm6
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 and org.Dm.eg.db_3.5.0.
A GRanges with all the TSSs for hg19. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.hg19tss.hg19
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz
A GRanges with all the TSSs for hg38. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.hg38tss.hg38
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.metadata.EntrezGene.gz
A GRanges with all the TSSs for mm10. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.mm10tss.mm10
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz
A GRanges with all the TSSs for mm9. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.mm9tss.mm9
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz
A GRanges with all the TSSs for rn4. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.rn4tss.rn4
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.
A GRanges with all the TSSs for rn5. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.rn5tss.rn5
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 and org.Rn.eg.db_3.5.0.
A GRanges with all the TSSs for rn6. Primarily used in the assign_peaks() function to report distance of a peak to the nearest TSS. Also used to build the QC plot with distribution of peaks to TSSs.
tss.rn6tss.rn6
A GRanges object with the following mcols:
The Entrez ID for the TSS
The gene symbol for the TSS
R packages: TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 and org.Rn.eg.db_3.5.0.