Package: chipenrich.data 2.36.0

Kai Wang

chipenrich.data: Companion package to chipenrich

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]

chipenrich.data_2.36.0.tar.gz
chipenrich.data_2.36.0.tar.gz(r-4.7-any)chipenrich.data_2.36.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
chipenrich.data/json (API)

# Install 'chipenrich.data' in R:

install.packages('chipenrich.data', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

enhancer.dnase_thurman.0 - Enhancer locations
gene.enh.desc - Gene-Enhancer descriptives
gene.enh.desc - Gene-Enhancer descriptives
gene.enh.desc - Gene-Enhancer descriptives
geneset.biocarta_pathway.hsa - Geneset.biocarta_pathway.hsa genesets for BioCarta
geneset.biocarta_pathway.mmu - Geneset.biocarta_pathway.mmu
geneset.biocarta_pathway.rno - Geneset.biocarta_pathway.rno
geneset.ctd.hsa - Geneset.ctd.hsa genesets for Comparative Toxicogenomics Database
geneset.ctd.mmu - Geneset.ctd.mmu genesets for Comparative Toxicogenomics Database
geneset.cytoband.hsa - Geneset.cytoband.hsa
geneset.drug_bank.hsa - Geneset.drug_bank.hsa genesets for DrugBank
geneset.drug_bank.mmu - Geneset.drug_bank.mmu
geneset.drug_bank.rno - Geneset.drug_bank.rno
geneset.GOBP.dme - Geneset.GOBP.dme genesets for Drosophila melanogaster
geneset.GOBP.dre - Geneset.GOBP.dre genesets for Danio rerio
geneset.GOBP.hsa - Geneset.GOBP.hsa genesets for Homo sapiens
geneset.GOBP.mmu - Geneset.GOBP.mmu genesets for Mus musculus
geneset.GOBP.rno - Geneset.GOBP.rno genesets for Rattus norvegicus
geneset.GOCC.dme - Geneset.GOCC.dme genesets for Drosophila melanogaster
geneset.GOCC.dre - Geneset.GOCC.dre genesets for Danio rerio
geneset.GOCC.hsa - Geneset.GOCC.hsa genesets for Homo sapiens
geneset.GOCC.mmu - Geneset.GOCC.mmu genesets for Mus musculus
geneset.GOCC.rno - Geneset.GOCC.rno genesets for Rattus norvegicus
geneset.GOMF.dme - Geneset.GOMF.dme genesets for Drosophila melanogaster
geneset.GOMF.dre - Geneset.GOMF.dre genesets for Danio rerio
geneset.GOMF.hsa - Geneset.GOMF.hsa genesets for Homo sapiens
geneset.GOMF.mmu - Geneset.GOMF.mmu genesets for Mus musculus
geneset.GOMF.rno - Geneset.GOMF.rno genesets for Rattus norvegicus
geneset.hallmark.hsa - Geneset.hallmark.hsa genesets for Hallmark
geneset.immunologic.hsa - Geneset.immunologic.hsa genesets for Immunologic Signatures
geneset.kegg_pathway.hsa - Geneset.kegg_pathway.hsa genesets for KEGG Pathways
geneset.kegg_pathway.mmu - Geneset.kegg_pathway.mmu
geneset.kegg_pathway.rno - Geneset.kegg_pathway.rno
geneset.mesh.hsa - Geneset.mesh.hsa
geneset.mesh.mmu - Geneset.mesh.mmu
geneset.mesh.rno - Geneset.mesh.rno
geneset.metabolite.hsa - Geneset.metabolite.hsa
geneset.metabolite.mmu - Geneset.metabolite.mmu
geneset.metabolite.rno - Geneset.metabolite.rno
geneset.microrna.hsa - Geneset.microrna.hsa genesets for MicroRNA Targets
geneset.oncogenic.hsa - Geneset.oncogenic.hsa genesets for Oncogenic Signatures
geneset.panther_pathway.hsa - Geneset.panther_pathway.hsa
geneset.panther_pathway.mmu - Geneset.panther_pathway.mmu
geneset.panther_pathway.rno - Geneset.panther_pathway.rno
geneset.pfam.hsa - Geneset.pfam.hsa genesets for Pfam
geneset.pfam.mmu - Geneset.pfam.mmu
geneset.pfam.rno - Geneset.pfam.rno
geneset.protein_interaction_biogrid.hsa - Geneset.protein_interaction_biogrid.hsa genesets for BioGRID Protein Interactions
geneset.reactome.dme - Geneset.reactome.dme genesets for Drosophila melanogaster
geneset.reactome.dre - Geneset.reactome.dre genesets for Danio rerio
geneset.reactome.hsa - Geneset.reactome.hsa genesets for Homo sapiens
geneset.reactome.mmu - Geneset.reactome.mmu genesets for Mus musculus
geneset.reactome.rno - Geneset.reactome.rno genesets for Rattus norvegicus
geneset.transcription_factors.hsa - Geneset.transcription_factors.hsa genesets for Transcription Factor Targets
geneset.transcription_factors.mmu - Geneset.transcription_factors.mmu
geneset.transcription_factors.rno - Geneset.transcription_factors.rno
locusdef.danRer10.10kb - Locusdef.danRer10.10kb locus definition
locusdef.danRer10.10kb_outside - Locusdef.danRer10.10kb_outside locus definition
locusdef.danRer10.10kb_outside_upstream - Locusdef.danRer10.10kb_outside_upstream locus definition
locusdef.danRer10.1kb - Locusdef.danRer10.1kb locus definition
locusdef.danRer10.1kb_outside - Locusdef.danRer10.1kb_outside locus definition
locusdef.danRer10.1kb_outside_upstream - Locusdef.danRer10.1kb_outside_upstream locus definition
locusdef.danRer10.5kb - Locusdef.danRer10.5kb locus definition
locusdef.danRer10.5kb_outside - Locusdef.danRer10.5kb_outside locus definition
locusdef.danRer10.5kb_outside_upstream - Locusdef.danRer10.5kb_outside_upstream locus definition
locusdef.danRer10.exon - Locusdef.danRer10.exon locus definition
locusdef.danRer10.intron - Locusdef.danRer10.intron locus definition
locusdef.danRer10.nearest_gene - Locusdef.danRer10.nearest_gene locus definition
locusdef.danRer10.nearest_tss - Locusdef.danRer10.nearest_tss locus definition
locusdef.dm3.10kb - Locusdef.dm3.10kb locus definition
locusdef.dm3.10kb_outside - Locusdef.dm3.10kb_outside locus definition
locusdef.dm3.10kb_outside_upstream - Locusdef.dm3.10kb_outside_upstream locus definition
locusdef.dm3.1kb - Locusdef.dm3.1kb locus definition
locusdef.dm3.1kb_outside - Locusdef.dm3.1kb_outside locus definition
locusdef.dm3.1kb_outside_upstream - Locusdef.dm3.1kb_outside_upstream locus definition
locusdef.dm3.5kb - Locusdef.dm3.5kb locus definition
locusdef.dm3.5kb_outside - Locusdef.dm3.5kb_outside locus definition
locusdef.dm3.5kb_outside_upstream - Locusdef.dm3.5kb_outside_upstream locus definition
locusdef.dm3.exon - Locusdef.dm3.exon locus definition
locusdef.dm3.intron - Locusdef.dm3.intron locus definition
locusdef.dm3.nearest_gene - Locusdef.dm3.nearest_gene locus definition
locusdef.dm3.nearest_tss - Locusdef.dm3.nearest_tss locus definition
locusdef.dm6.10kb - Locusdef.dm6.10kb locus definition
locusdef.dm6.10kb_outside - Locusdef.dm6.10kb_outside locus definition
locusdef.dm6.10kb_outside_upstream - Locusdef.dm6.10kb_outside_upstream locus definition
locusdef.dm6.1kb - Locusdef.dm6.1kb locus definition
locusdef.dm6.1kb_outside - Locusdef.dm6.1kb_outside locus definition
locusdef.dm6.1kb_outside_upstream - Locusdef.dm6.1kb_outside_upstream locus definition
locusdef.dm6.5kb - Locusdef.dm6.5kb locus definition
locusdef.dm6.5kb_outside - Locusdef.dm6.5kb_outside locus definition
locusdef.dm6.5kb_outside_upstream - Locusdef.dm6.5kb_outside_upstream locus definition
locusdef.dm6.exon - Locusdef.dm6.exon locus definition
locusdef.dm6.intron - Locusdef.dm6.intron locus definition
locusdef.dm6.nearest_gene - Locusdef.dm6.nearest_gene locus definition
locusdef.dm6.nearest_tss - Locusdef.dm6.nearest_tss locus definition
locusdef.hg19.10kb - Locusdef.hg19.10kb locus definition
locusdef.hg19.10kb_outside - Locusdef.hg19.10kb_outside locus definition
locusdef.hg19.10kb_outside_upstream - Locusdef.hg19.10kb_outside_upstream locus definition
locusdef.hg19.1kb - Locusdef.hg19.1kb locus definition
locusdef.hg19.1kb_outside - Locusdef.hg19.1kb_outside locus definition
locusdef.hg19.1kb_outside_upstream - Locusdef.hg19.1kb_outside_upstream locus definition
locusdef.hg19.5kb - Locusdef.hg19.5kb locus definition
locusdef.hg19.5kb_outside - Locusdef.hg19.5kb_outside locus definition
locusdef.hg19.5kb_outside_upstream - Locusdef.hg19.5kb_outside_upstream locus definition
locusdef.hg19.exon - Locusdef.hg19.exon locus definition
locusdef.hg19.intron - Locusdef.hg19.intron locus definition
locusdef.hg19.nearest_gene - Locusdef.hg19.nearest_gene locus definition
locusdef.hg19.nearest_tss - Locusdef.hg19.nearest_tss locus definition
locusdef.hg38.10kb - Locusdef.hg38.10kb locus definition
locusdef.hg38.10kb_outside - Locusdef.hg38.10kb_outside locus definition
locusdef.hg38.10kb_outside_upstream - Locusdef.hg38.10kb_outside_upstream locus definition
locusdef.hg38.1kb - Locusdef.hg38.1kb locus definition
locusdef.hg38.1kb_outside - Locusdef.hg38.1kb_outside locus definition
locusdef.hg38.1kb_outside_upstream - Locusdef.hg38.1kb_outside_upstream locus definition
locusdef.hg38.5kb - Locusdef.hg38.5kb locus definition
locusdef.hg38.5kb_outside - Locusdef.hg38.5kb_outside locus definition
locusdef.hg38.5kb_outside_upstream - Locusdef.hg38.5kb_outside_upstream locus definition
locusdef.hg38.exon - Locusdef.hg38.exon locus definition
locusdef.hg38.intron - Locusdef.hg38.intron locus definition
locusdef.hg38.nearest_gene - Locusdef.hg38.nearest_gene locus definition
locusdef.hg38.nearest_tss - Locusdef.hg38.nearest_tss locus definition
locusdef.mm10.10kb - Locusdef.mm10.10kb locus definition
locusdef.mm10.10kb_outside - Locusdef.mm10.10kb_outside locus definition
locusdef.mm10.10kb_outside_upstream - Locusdef.mm10.10kb_outside_upstream locus definition
locusdef.mm10.1kb - Locusdef.mm10.1kb locus definition
locusdef.mm10.1kb_outside - Locusdef.mm10.1kb_outside locus definition
locusdef.mm10.1kb_outside_upstream - Locusdef.mm10.1kb_outside_upstream locus definition
locusdef.mm10.5kb - Locusdef.mm10.5kb locus definition
locusdef.mm10.5kb_outside - Locusdef.mm10.5kb_outside locus definition
locusdef.mm10.5kb_outside_upstream - Locusdef.mm10.5kb_outside_upstream locus definition
locusdef.mm10.exon - Locusdef.mm10.exon locus definition
locusdef.mm10.intron - Locusdef.mm10.intron locus definition
locusdef.mm10.nearest_gene - Locusdef.mm10.nearest_gene locus definition
locusdef.mm10.nearest_tss - Locusdef.mm10.nearest_tss locus definition
locusdef.mm9.10kb - Locusdef.mm9.10kb locus definition
locusdef.mm9.10kb_outside - Locusdef.mm9.10kb_outside locus definition
locusdef.mm9.10kb_outside_upstream - Locusdef.mm9.10kb_outside_upstream locus definition
locusdef.mm9.1kb - Locusdef.mm9.1kb locus definition
locusdef.mm9.1kb_outside - Locusdef.mm9.1kb_outside locus definition
locusdef.mm9.1kb_outside_upstream - Locusdef.mm9.1kb_outside_upstream locus definition
locusdef.mm9.5kb - Locusdef.mm9.5kb locus definition
locusdef.mm9.5kb_outside - Locusdef.mm9.5kb_outside locus definition
locusdef.mm9.5kb_outside_upstream - Locusdef.mm9.5kb_outside_upstream locus definition
locusdef.mm9.exon - Locusdef.mm9.exon locus definition
locusdef.mm9.intron - Locusdef.mm9.intron locus definition
locusdef.mm9.nearest_gene - Locusdef.mm9.nearest_gene locus definition
locusdef.mm9.nearest_tss - Locusdef.mm9.nearest_tss locus definition
locusdef.rn4.10kb - Locusdef.rn4.10kb locus definition
locusdef.rn4.10kb_outside - Locusdef.rn4.10kb_outside locus definition
locusdef.rn4.10kb_outside_upstream - Locusdef.rn4.10kb_outside_upstream locus definition
locusdef.rn4.1kb - Locusdef.rn4.1kb locus definition
locusdef.rn4.1kb_outside - Locusdef.rn4.1kb_outside locus definition
locusdef.rn4.1kb_outside_upstream - Locusdef.rn4.1kb_outside_upstream locus definition
locusdef.rn4.5kb - Locusdef.rn4.5kb locus definition
locusdef.rn4.5kb_outside - Locusdef.rn4.5kb_outside locus definition
locusdef.rn4.5kb_outside_upstream - Locusdef.rn4.5kb_outside_upstream locus definition
locusdef.rn4.exon - Locusdef.rn4.exon locus definition
locusdef.rn4.intron - Locusdef.rn4.intron locus definition
locusdef.rn4.nearest_gene - Locusdef.rn4.nearest_gene locus definition
locusdef.rn4.nearest_tss - Locusdef.rn4.nearest_tss locus definition
locusdef.rn5.10kb - Locusdef.rn5.10kb locus definition
locusdef.rn5.10kb_outside - Locusdef.rn5.10kb_outside locus definition
locusdef.rn5.10kb_outside_upstream - Locusdef.rn5.10kb_outside_upstream locus definition
locusdef.rn5.1kb - Locusdef.rn5.1kb locus definition
locusdef.rn5.1kb_outside - Locusdef.rn5.1kb_outside locus definition
locusdef.rn5.1kb_outside_upstream - Locusdef.rn5.1kb_outside_upstream locus definition
locusdef.rn5.5kb - Locusdef.rn5.5kb locus definition
locusdef.rn5.5kb_outside - Locusdef.rn5.5kb_outside locus definition
locusdef.rn5.5kb_outside_upstream - Locusdef.rn5.5kb_outside_upstream locus definition
locusdef.rn5.exon - Locusdef.rn5.exon locus definition
locusdef.rn5.intron - Locusdef.rn5.intron locus definition
locusdef.rn5.nearest_gene - Locusdef.rn5.nearest_gene locus definition
locusdef.rn5.nearest_tss - Locusdef.rn5.nearest_tss locus definition
locusdef.rn6.10kb - Locusdef.rn6.10kb locus definition
locusdef.rn6.10kb_outside - Locusdef.rn6.10kb_outside locus definition
locusdef.rn6.10kb_outside_upstream - Locusdef.rn6.10kb_outside_upstream locus definition
locusdef.rn6.1kb - Locusdef.rn6.1kb locus definition
locusdef.rn6.1kb_outside - Locusdef.rn6.1kb_outside locus definition
locusdef.rn6.1kb_outside_upstream - Locusdef.rn6.1kb_outside_upstream locus definition
locusdef.rn6.5kb - Locusdef.rn6.5kb locus definition
locusdef.rn6.5kb_outside - Locusdef.rn6.5kb_outside locus definition
locusdef.rn6.5kb_outside_upstream - Locusdef.rn6.5kb_outside_upstream locus definition
locusdef.rn6.exon - Locusdef.rn6.exon locus definition
locusdef.rn6.intron - Locusdef.rn6.intron locus definition
locusdef.rn6.nearest_gene - Locusdef.rn6.nearest_gene locus definition
locusdef.rn6.nearest_tss - Locusdef.rn6.nearest_tss locus definition
mappa.hg19.10kb.100mer - Mappa.hg19.10kb.100mer
mappa.hg19.10kb.24mer - Mappa.hg19.10kb.24mer
mappa.hg19.10kb.36mer - Mappa.hg19.10kb.36mer
mappa.hg19.10kb.40mer - Mappa.hg19.10kb.40mer
mappa.hg19.10kb.50mer - Mappa.hg19.10kb.50mer
mappa.hg19.10kb.75mer - Mappa.hg19.10kb.75mer
mappa.hg19.1kb.100mer - Mappa.hg19.1kb.100mer
mappa.hg19.1kb.24mer - Mappa.hg19.1kb.24mer
mappa.hg19.1kb.36mer - Mappa.hg19.1kb.36mer
mappa.hg19.1kb.40mer - Mappa.hg19.1kb.40mer
mappa.hg19.1kb.50mer - Mappa.hg19.1kb.50mer
mappa.hg19.1kb.75mer - Mappa.hg19.1kb.75mer
mappa.hg19.5kb.100mer - Mappa.hg19.5kb.100mer
mappa.hg19.5kb.24mer - Mappa.hg19.5kb.24mer
mappa.hg19.5kb.36mer - Mappa.hg19.5kb.36mer
mappa.hg19.5kb.40mer - Mappa.hg19.5kb.40mer
mappa.hg19.5kb.50mer - Mappa.hg19.5kb.50mer
mappa.hg19.5kb.75mer - Mappa.hg19.5kb.75mer
mappa.hg19.exon.100mer - Mappa.hg19.exon.100mer
mappa.hg19.exon.24mer - Mappa.hg19.exon.24mer
mappa.hg19.exon.36mer - Mappa.hg19.exon.36mer
mappa.hg19.exon.40mer - Mappa.hg19.exon.40mer
mappa.hg19.exon.50mer - Mappa.hg19.exon.50mer
mappa.hg19.exon.75mer - Mappa.hg19.exon.75mer
mappa.hg19.intron.100mer - Mappa.hg19.intron.100mer
mappa.hg19.intron.24mer - Mappa.hg19.intron.24mer
mappa.hg19.intron.36mer - Mappa.hg19.intron.36mer
mappa.hg19.intron.40mer - Mappa.hg19.intron.40mer
mappa.hg19.intron.50mer - Mappa.hg19.intron.50mer
mappa.hg19.intron.75mer - Mappa.hg19.intron.75mer
mappa.hg19.nearest_gene.100mer - Mappa.hg19.nearest_gene.100mer
mappa.hg19.nearest_gene.24mer - Mappa.hg19.nearest_gene.24mer
mappa.hg19.nearest_gene.36mer - Mappa.hg19.nearest_gene.36mer
mappa.hg19.nearest_gene.40mer - Mappa.hg19.nearest_gene.40mer
mappa.hg19.nearest_gene.50mer - Mappa.hg19.nearest_gene.50mer
mappa.hg19.nearest_gene.75mer - Mappa.hg19.nearest_gene.75mer
mappa.hg19.nearest_tss.100mer - Mappa.hg19.nearest_tss.100mer
mappa.hg19.nearest_tss.24mer - Mappa.hg19.nearest_tss.24mer
mappa.hg19.nearest_tss.36mer - Mappa.hg19.nearest_tss.36mer
mappa.hg19.nearest_tss.40mer - Mappa.hg19.nearest_tss.40mer
mappa.hg19.nearest_tss.50mer - Mappa.hg19.nearest_tss.50mer
mappa.hg19.nearest_tss.75mer - Mappa.hg19.nearest_tss.75mer
mappa.mm9.10kb.100mer - Mappa.mm9.10kb.100mer
mappa.mm9.10kb.36mer - Mappa.mm9.10kb.36mer
mappa.mm9.10kb.40mer - Mappa.mm9.10kb.40mer
mappa.mm9.10kb.50mer - Mappa.mm9.10kb.50mer
mappa.mm9.10kb.75mer - Mappa.mm9.10kb.75mer
mappa.mm9.1kb.100mer - Mappa.mm9.1kb.100mer
mappa.mm9.1kb.36mer - Mappa.mm9.1kb.36mer
mappa.mm9.1kb.40mer - Mappa.mm9.1kb.40mer
mappa.mm9.1kb.50mer - Mappa.mm9.1kb.50mer
mappa.mm9.1kb.75mer - Mappa.mm9.1kb.75mer
mappa.mm9.5kb.100mer - Mappa.mm9.5kb.100mer
mappa.mm9.5kb.36mer - Mappa.mm9.5kb.36mer
mappa.mm9.5kb.40mer - Mappa.mm9.5kb.40mer
mappa.mm9.5kb.50mer - Mappa.mm9.5kb.50mer
mappa.mm9.5kb.75mer - Mappa.mm9.5kb.75mer
mappa.mm9.exon.100mer - Mappa.mm9.exon.100mer
mappa.mm9.exon.36mer - Mappa.mm9.exon.36mer
mappa.mm9.exon.40mer - Mappa.mm9.exon.40mer
mappa.mm9.exon.50mer - Mappa.mm9.exon.50mer
mappa.mm9.exon.75mer - Mappa.mm9.exon.75mer
mappa.mm9.intron.100mer - Mappa.mm9.intron.100mer
mappa.mm9.intron.36mer - Mappa.mm9.intron.36mer
mappa.mm9.intron.40mer - Mappa.mm9.intron.40mer
mappa.mm9.intron.50mer - Mappa.mm9.intron.50mer
mappa.mm9.intron.75mer - Mappa.mm9.intron.75mer
mappa.mm9.nearest_gene.100mer - Mappa.mm9.nearest_gene.100mer
mappa.mm9.nearest_gene.36mer - Mappa.mm9.nearest_gene.36mer
mappa.mm9.nearest_gene.40mer - Mappa.mm9.nearest_gene.40mer
mappa.mm9.nearest_gene.50mer - Mappa.mm9.nearest_gene.50mer
mappa.mm9.nearest_gene.75mer - Mappa.mm9.nearest_gene.75mer
mappa.mm9.nearest_tss.100mer - Mappa.mm9.nearest_tss.100mer
mappa.mm9.nearest_tss.36mer - Mappa.mm9.nearest_tss.36mer
mappa.mm9.nearest_tss.40mer - Mappa.mm9.nearest_tss.40mer
mappa.mm9.nearest_tss.50mer - Mappa.mm9.nearest_tss.50mer
mappa.mm9.nearest_tss.75mer - Mappa.mm9.nearest_tss.75mer
peaks_E2F4 - ChIP-seq Peaks for the E2F4 Transcription Factor
peaks_H3K4me3_GM12878 - ChIP-seq Peaks for the Histone Modification H3K4me3 in GM12878
spline.log_dtss.90ENCODE - DTSS Spline adjustment
tss.danRer10 - Tss.danRer10 TSS locations
tss.dm3 - Tss.dm3 TSS locations
tss.dm6 - Tss.dm6 TSS locations
tss.hg19 - Tss.hg19 TSS locations
tss.hg38 - Tss.hg38 TSS locations
tss.mm10 - Tss.mm10 TSS locations
tss.mm9 - Tss.mm9 TSS locations
tss.rn4 - Tss.rn4 TSS locations
tss.rn5 - Tss.rn5 TSS locations
tss.rn6 - Tss.rn6 TSS locations

On BioConductor:chipenrich.data-2.37.0(data/experiment 3.24)chipenrich.data-2.36.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipseq epigenetics functionalgenomics genesetenrichment histonemodification regression datapkg

4.08 score 1 packages 7 scripts 2 mentions 0 exports 80 dependencies

Last updated from:d71fb8bd3a (on RELEASE_3_23). Checks:3 WARNING, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	WARNING	578
linux-devel	WARNING	922
source / vignettes	OK	1026
linux-release	WARNING	977

Exports:

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli clipr codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges glue hms httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress R6 RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys tibble tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML XVector yaml

chipenrich.data

Locus definitions | Genesets | TSS data | Mappability data | Example data for chipenrich

Rendered fromchipenrich.data-vignette.Rmdusingknitr::rmarkdown

Last update: 2017-03-21
Started: 2016-08-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
chipenrich.data: Data for chipenrich: gene set enrichment analysis for ChIP-seq data	chipenrich.data-package chipenrich.data
Enhancer locations	enhancer.dnase_thurman.0
Gene-Enhancer descriptives	gene.enh.desc
Class '"GeneSet"'	GeneSet-class
geneset.biocarta_pathway.hsa genesets for BioCarta	geneset.biocarta_pathway.hsa
geneset.biocarta_pathway.mmu	geneset.biocarta_pathway.mmu
geneset.biocarta_pathway.rno	geneset.biocarta_pathway.rno
geneset.ctd.hsa genesets for Comparative Toxicogenomics Database	geneset.ctd.hsa
geneset.ctd.mmu genesets for Comparative Toxicogenomics Database	geneset.ctd.mmu
geneset.cytoband.hsa	geneset.cytoband.hsa
geneset.drug_bank.hsa genesets for DrugBank	geneset.drug_bank.hsa
geneset.drug_bank.mmu	geneset.drug_bank.mmu
geneset.drug_bank.rno	geneset.drug_bank.rno
geneset.GOBP.dme genesets for Drosophila melanogaster	geneset.GOBP.dme
geneset.GOBP.dre genesets for Danio rerio	geneset.GOBP.dre
geneset.GOBP.hsa genesets for Homo sapiens	geneset.GOBP.hsa
geneset.GOBP.mmu genesets for Mus musculus	geneset.GOBP.mmu
geneset.GOBP.rno genesets for Rattus norvegicus	geneset.GOBP.rno
geneset.GOCC.dme genesets for Drosophila melanogaster	geneset.GOCC.dme
geneset.GOCC.dre genesets for Danio rerio	geneset.GOCC.dre
geneset.GOCC.hsa genesets for Homo sapiens	geneset.GOCC.hsa
geneset.GOCC.mmu genesets for Mus musculus	geneset.GOCC.mmu
geneset.GOCC.rno genesets for Rattus norvegicus	geneset.GOCC.rno
geneset.GOMF.dme genesets for Drosophila melanogaster	geneset.GOMF.dme
geneset.GOMF.dre genesets for Danio rerio	geneset.GOMF.dre
geneset.GOMF.hsa genesets for Homo sapiens	geneset.GOMF.hsa
geneset.GOMF.mmu genesets for Mus musculus	geneset.GOMF.mmu
geneset.GOMF.rno genesets for Rattus norvegicus	geneset.GOMF.rno
geneset.hallmark.hsa genesets for Hallmark (MSigDB)	geneset.hallmark.hsa
geneset.immunologic.hsa genesets for Immunologic Signatures (MSigDB)	geneset.immunologic.hsa
geneset.kegg_pathway.hsa genesets for KEGG Pathways	geneset.kegg_pathway.hsa
geneset.kegg_pathway.mmu	geneset.kegg_pathway.mmu
geneset.kegg_pathway.rno	geneset.kegg_pathway.rno
geneset.mesh.hsa	geneset.mesh.hsa
geneset.mesh.mmu	geneset.mesh.mmu
geneset.mesh.rno	geneset.mesh.rno
geneset.metabolite.hsa	geneset.metabolite.hsa
geneset.metabolite.mmu	geneset.metabolite.mmu
geneset.metabolite.rno	geneset.metabolite.rno
geneset.microrna.hsa genesets for MicroRNA Targets (MSigDB)	geneset.microrna.hsa
geneset.oncogenic.hsa genesets for Oncogenic Signatures (MSigDB)	geneset.oncogenic.hsa
geneset.panther_pathway.hsa	geneset.panther_pathway.hsa
geneset.panther_pathway.mmu	geneset.panther_pathway.mmu
geneset.panther_pathway.rno	geneset.panther_pathway.rno
geneset.pfam.hsa genesets for Pfam	geneset.pfam.hsa
geneset.pfam.mmu	geneset.pfam.mmu
geneset.pfam.rno	geneset.pfam.rno
geneset.protein_interaction_biogrid.hsa genesets for BioGRID Protein Interactions	geneset.protein_interaction_biogrid.hsa
geneset.reactome.dme genesets for Drosophila melanogaster	geneset.reactome.dme
geneset.reactome.dre genesets for Danio rerio	geneset.reactome.dre
geneset.reactome.hsa genesets for Homo sapiens	geneset.reactome.hsa
geneset.reactome.mmu genesets for Mus musculus	geneset.reactome.mmu
geneset.reactome.rno genesets for Rattus norvegicus	geneset.reactome.rno
geneset.transcription_factors.hsa genesets for Transcription Factor Targets (MSigDB)	geneset.transcription_factors.hsa
geneset.transcription_factors.mmu	geneset.transcription_factors.mmu
geneset.transcription_factors.rno	geneset.transcription_factors.rno
locusdef.danRer10.10kb locus definition	locusdef.danRer10.10kb
locusdef.danRer10.10kb_outside locus definition	locusdef.danRer10.10kb_outside
locusdef.danRer10.10kb_outside_upstream locus definition	locusdef.danRer10.10kb_outside_upstream
locusdef.danRer10.1kb locus definition	locusdef.danRer10.1kb
locusdef.danRer10.1kb_outside locus definition	locusdef.danRer10.1kb_outside
locusdef.danRer10.1kb_outside_upstream locus definition	locusdef.danRer10.1kb_outside_upstream
locusdef.danRer10.5kb locus definition	locusdef.danRer10.5kb
locusdef.danRer10.5kb_outside locus definition	locusdef.danRer10.5kb_outside
locusdef.danRer10.5kb_outside_upstream locus definition	locusdef.danRer10.5kb_outside_upstream
locusdef.danRer10.exon locus definition	locusdef.danRer10.exon
locusdef.danRer10.intron locus definition	locusdef.danRer10.intron
locusdef.danRer10.nearest_gene locus definition	locusdef.danRer10.nearest_gene
locusdef.danRer10.nearest_tss locus definition	locusdef.danRer10.nearest_tss
locusdef.dm3.10kb locus definition	locusdef.dm3.10kb
locusdef.dm3.10kb_outside locus definition	locusdef.dm3.10kb_outside
locusdef.dm3.10kb_outside_upstream locus definition	locusdef.dm3.10kb_outside_upstream
locusdef.dm3.1kb locus definition	locusdef.dm3.1kb
locusdef.dm3.1kb_outside locus definition	locusdef.dm3.1kb_outside
locusdef.dm3.1kb_outside_upstream locus definition	locusdef.dm3.1kb_outside_upstream
locusdef.dm3.5kb locus definition	locusdef.dm3.5kb
locusdef.dm3.5kb_outside locus definition	locusdef.dm3.5kb_outside
locusdef.dm3.5kb_outside_upstream locus definition	locusdef.dm3.5kb_outside_upstream
locusdef.dm3.exon locus definition	locusdef.dm3.exon
locusdef.dm3.intron locus definition	locusdef.dm3.intron
locusdef.dm3.nearest_gene locus definition	locusdef.dm3.nearest_gene
locusdef.dm3.nearest_tss locus definition	locusdef.dm3.nearest_tss
locusdef.dm6.10kb locus definition	locusdef.dm6.10kb
locusdef.dm6.10kb_outside locus definition	locusdef.dm6.10kb_outside
locusdef.dm6.10kb_outside_upstream locus definition	locusdef.dm6.10kb_outside_upstream
locusdef.dm6.1kb locus definition	locusdef.dm6.1kb
locusdef.dm6.1kb_outside locus definition	locusdef.dm6.1kb_outside
locusdef.dm6.1kb_outside_upstream locus definition	locusdef.dm6.1kb_outside_upstream
locusdef.dm6.5kb locus definition	locusdef.dm6.5kb
locusdef.dm6.5kb_outside locus definition	locusdef.dm6.5kb_outside
locusdef.dm6.5kb_outside_upstream locus definition	locusdef.dm6.5kb_outside_upstream
locusdef.dm6.exon locus definition	locusdef.dm6.exon
locusdef.dm6.intron locus definition	locusdef.dm6.intron
locusdef.dm6.nearest_gene locus definition	locusdef.dm6.nearest_gene
locusdef.dm6.nearest_tss locus definition	locusdef.dm6.nearest_tss
locusdef.hg19.10kb locus definition	locusdef.hg19.10kb
locusdef.hg19.10kb_outside locus definition	locusdef.hg19.10kb_outside
locusdef.hg19.10kb_outside_upstream locus definition	locusdef.hg19.10kb_outside_upstream
locusdef.hg19.1kb locus definition	locusdef.hg19.1kb
locusdef.hg19.1kb_outside locus definition	locusdef.hg19.1kb_outside
locusdef.hg19.1kb_outside_upstream locus definition	locusdef.hg19.1kb_outside_upstream
locusdef.hg19.5kb locus definition	locusdef.hg19.5kb
locusdef.hg19.5kb_outside locus definition	locusdef.hg19.5kb_outside
locusdef.hg19.5kb_outside_upstream locus definition	locusdef.hg19.5kb_outside_upstream
locusdef.hg19.exon locus definition	locusdef.hg19.exon
locusdef.hg19.intron locus definition	locusdef.hg19.intron
locusdef.hg19.nearest_gene locus definition	locusdef.hg19.nearest_gene
locusdef.hg19.nearest_tss locus definition	locusdef.hg19.nearest_tss
locusdef.hg38.10kb locus definition	locusdef.hg38.10kb
locusdef.hg38.10kb_outside locus definition	locusdef.hg38.10kb_outside
locusdef.hg38.10kb_outside_upstream locus definition	locusdef.hg38.10kb_outside_upstream
locusdef.hg38.1kb locus definition	locusdef.hg38.1kb
locusdef.hg38.1kb_outside locus definition	locusdef.hg38.1kb_outside
locusdef.hg38.1kb_outside_upstream locus definition	locusdef.hg38.1kb_outside_upstream
locusdef.hg38.5kb locus definition	locusdef.hg38.5kb
locusdef.hg38.5kb_outside locus definition	locusdef.hg38.5kb_outside
locusdef.hg38.5kb_outside_upstream locus definition	locusdef.hg38.5kb_outside_upstream
locusdef.hg38.exon locus definition	locusdef.hg38.exon
locusdef.hg38.intron locus definition	locusdef.hg38.intron
locusdef.hg38.nearest_gene locus definition	locusdef.hg38.nearest_gene
locusdef.hg38.nearest_tss locus definition	locusdef.hg38.nearest_tss
locusdef.mm10.10kb locus definition	locusdef.mm10.10kb
locusdef.mm10.10kb_outside locus definition	locusdef.mm10.10kb_outside
locusdef.mm10.10kb_outside_upstream locus definition	locusdef.mm10.10kb_outside_upstream
locusdef.mm10.1kb locus definition	locusdef.mm10.1kb
locusdef.mm10.1kb_outside locus definition	locusdef.mm10.1kb_outside
locusdef.mm10.1kb_outside_upstream locus definition	locusdef.mm10.1kb_outside_upstream
locusdef.mm10.5kb locus definition	locusdef.mm10.5kb
locusdef.mm10.5kb_outside locus definition	locusdef.mm10.5kb_outside
locusdef.mm10.5kb_outside_upstream locus definition	locusdef.mm10.5kb_outside_upstream
locusdef.mm10.exon locus definition	locusdef.mm10.exon
locusdef.mm10.intron locus definition	locusdef.mm10.intron
locusdef.mm10.nearest_gene locus definition	locusdef.mm10.nearest_gene
locusdef.mm10.nearest_tss locus definition	locusdef.mm10.nearest_tss
locusdef.mm9.10kb locus definition	locusdef.mm9.10kb
locusdef.mm9.10kb_outside locus definition	locusdef.mm9.10kb_outside
locusdef.mm9.10kb_outside_upstream locus definition	locusdef.mm9.10kb_outside_upstream
locusdef.mm9.1kb locus definition	locusdef.mm9.1kb
locusdef.mm9.1kb_outside locus definition	locusdef.mm9.1kb_outside
locusdef.mm9.1kb_outside_upstream locus definition	locusdef.mm9.1kb_outside_upstream
locusdef.mm9.5kb locus definition	locusdef.mm9.5kb
locusdef.mm9.5kb_outside locus definition	locusdef.mm9.5kb_outside
locusdef.mm9.5kb_outside_upstream locus definition	locusdef.mm9.5kb_outside_upstream
locusdef.mm9.exon locus definition	locusdef.mm9.exon
locusdef.mm9.intron locus definition	locusdef.mm9.intron
locusdef.mm9.nearest_gene locus definition	locusdef.mm9.nearest_gene
locusdef.mm9.nearest_tss locus definition	locusdef.mm9.nearest_tss
locusdef.rn4.10kb locus definition	locusdef.rn4.10kb
locusdef.rn4.10kb_outside locus definition	locusdef.rn4.10kb_outside
locusdef.rn4.10kb_outside_upstream locus definition	locusdef.rn4.10kb_outside_upstream
locusdef.rn4.1kb locus definition	locusdef.rn4.1kb
locusdef.rn4.1kb_outside locus definition	locusdef.rn4.1kb_outside
locusdef.rn4.1kb_outside_upstream locus definition	locusdef.rn4.1kb_outside_upstream
locusdef.rn4.5kb locus definition	locusdef.rn4.5kb
locusdef.rn4.5kb_outside locus definition	locusdef.rn4.5kb_outside
locusdef.rn4.5kb_outside_upstream locus definition	locusdef.rn4.5kb_outside_upstream
locusdef.rn4.exon locus definition	locusdef.rn4.exon
locusdef.rn4.intron locus definition	locusdef.rn4.intron
locusdef.rn4.nearest_gene locus definition	locusdef.rn4.nearest_gene
locusdef.rn4.nearest_tss locus definition	locusdef.rn4.nearest_tss
locusdef.rn5.10kb locus definition	locusdef.rn5.10kb
locusdef.rn5.10kb_outside locus definition	locusdef.rn5.10kb_outside
locusdef.rn5.10kb_outside_upstream locus definition	locusdef.rn5.10kb_outside_upstream
locusdef.rn5.1kb locus definition	locusdef.rn5.1kb
locusdef.rn5.1kb_outside locus definition	locusdef.rn5.1kb_outside
locusdef.rn5.1kb_outside_upstream locus definition	locusdef.rn5.1kb_outside_upstream
locusdef.rn5.5kb locus definition	locusdef.rn5.5kb
locusdef.rn5.5kb_outside locus definition	locusdef.rn5.5kb_outside
locusdef.rn5.5kb_outside_upstream locus definition	locusdef.rn5.5kb_outside_upstream
locusdef.rn5.exon locus definition	locusdef.rn5.exon
locusdef.rn5.intron locus definition	locusdef.rn5.intron
locusdef.rn5.nearest_gene locus definition	locusdef.rn5.nearest_gene
locusdef.rn5.nearest_tss locus definition	locusdef.rn5.nearest_tss
locusdef.rn6.10kb locus definition	locusdef.rn6.10kb
locusdef.rn6.10kb_outside locus definition	locusdef.rn6.10kb_outside
locusdef.rn6.10kb_outside_upstream locus definition	locusdef.rn6.10kb_outside_upstream
locusdef.rn6.1kb locus definition	locusdef.rn6.1kb
locusdef.rn6.1kb_outside locus definition	locusdef.rn6.1kb_outside
locusdef.rn6.1kb_outside_upstream locus definition	locusdef.rn6.1kb_outside_upstream
locusdef.rn6.5kb locus definition	locusdef.rn6.5kb
locusdef.rn6.5kb_outside locus definition	locusdef.rn6.5kb_outside
locusdef.rn6.5kb_outside_upstream locus definition	locusdef.rn6.5kb_outside_upstream
locusdef.rn6.exon locus definition	locusdef.rn6.exon
locusdef.rn6.intron locus definition	locusdef.rn6.intron
locusdef.rn6.nearest_gene locus definition	locusdef.rn6.nearest_gene
locusdef.rn6.nearest_tss locus definition	locusdef.rn6.nearest_tss
Class '"LocusDefinition"'	LocusDefinition-class
mappa.hg19.10kb.100mer	mappa.hg19.10kb.100mer
mappa.hg19.10kb.24mer	mappa.hg19.10kb.24mer
mappa.hg19.10kb.36mer	mappa.hg19.10kb.36mer
mappa.hg19.10kb.40mer	mappa.hg19.10kb.40mer
mappa.hg19.10kb.50mer	mappa.hg19.10kb.50mer
mappa.hg19.10kb.75mer	mappa.hg19.10kb.75mer
mappa.hg19.1kb.100mer	mappa.hg19.1kb.100mer
mappa.hg19.1kb.24mer	mappa.hg19.1kb.24mer
mappa.hg19.1kb.36mer	mappa.hg19.1kb.36mer
mappa.hg19.1kb.40mer	mappa.hg19.1kb.40mer
mappa.hg19.1kb.50mer	mappa.hg19.1kb.50mer
mappa.hg19.1kb.75mer	mappa.hg19.1kb.75mer
mappa.hg19.5kb.100mer	mappa.hg19.5kb.100mer
mappa.hg19.5kb.24mer	mappa.hg19.5kb.24mer
mappa.hg19.5kb.36mer	mappa.hg19.5kb.36mer
mappa.hg19.5kb.40mer	mappa.hg19.5kb.40mer
mappa.hg19.5kb.50mer	mappa.hg19.5kb.50mer
mappa.hg19.5kb.75mer	mappa.hg19.5kb.75mer
mappa.hg19.exon.100mer	mappa.hg19.exon.100mer
mappa.hg19.exon.24mer	mappa.hg19.exon.24mer
mappa.hg19.exon.36mer	mappa.hg19.exon.36mer
mappa.hg19.exon.40mer	mappa.hg19.exon.40mer
mappa.hg19.exon.50mer	mappa.hg19.exon.50mer
mappa.hg19.exon.75mer	mappa.hg19.exon.75mer
mappa.hg19.intron.100mer	mappa.hg19.intron.100mer
mappa.hg19.intron.24mer	mappa.hg19.intron.24mer
mappa.hg19.intron.36mer	mappa.hg19.intron.36mer
mappa.hg19.intron.40mer	mappa.hg19.intron.40mer
mappa.hg19.intron.50mer	mappa.hg19.intron.50mer
mappa.hg19.intron.75mer	mappa.hg19.intron.75mer
mappa.hg19.nearest_gene.100mer	mappa.hg19.nearest_gene.100mer
mappa.hg19.nearest_gene.24mer	mappa.hg19.nearest_gene.24mer
mappa.hg19.nearest_gene.36mer	mappa.hg19.nearest_gene.36mer
mappa.hg19.nearest_gene.40mer	mappa.hg19.nearest_gene.40mer
mappa.hg19.nearest_gene.50mer	mappa.hg19.nearest_gene.50mer
mappa.hg19.nearest_gene.75mer	mappa.hg19.nearest_gene.75mer
mappa.hg19.nearest_tss.100mer	mappa.hg19.nearest_tss.100mer
mappa.hg19.nearest_tss.24mer	mappa.hg19.nearest_tss.24mer
mappa.hg19.nearest_tss.36mer	mappa.hg19.nearest_tss.36mer
mappa.hg19.nearest_tss.40mer	mappa.hg19.nearest_tss.40mer
mappa.hg19.nearest_tss.50mer	mappa.hg19.nearest_tss.50mer
mappa.hg19.nearest_tss.75mer	mappa.hg19.nearest_tss.75mer
mappa.mm9.10kb.100mer	mappa.mm9.10kb.100mer
mappa.mm9.10kb.36mer	mappa.mm9.10kb.36mer
mappa.mm9.10kb.40mer	mappa.mm9.10kb.40mer
mappa.mm9.10kb.50mer	mappa.mm9.10kb.50mer
mappa.mm9.10kb.75mer	mappa.mm9.10kb.75mer
mappa.mm9.1kb.100mer	mappa.mm9.1kb.100mer
mappa.mm9.1kb.36mer	mappa.mm9.1kb.36mer
mappa.mm9.1kb.40mer	mappa.mm9.1kb.40mer
mappa.mm9.1kb.50mer	mappa.mm9.1kb.50mer
mappa.mm9.1kb.75mer	mappa.mm9.1kb.75mer
mappa.mm9.5kb.100mer	mappa.mm9.5kb.100mer
mappa.mm9.5kb.36mer	mappa.mm9.5kb.36mer
mappa.mm9.5kb.40mer	mappa.mm9.5kb.40mer
mappa.mm9.5kb.50mer	mappa.mm9.5kb.50mer
mappa.mm9.5kb.75mer	mappa.mm9.5kb.75mer
mappa.mm9.exon.100mer	mappa.mm9.exon.100mer
mappa.mm9.exon.36mer	mappa.mm9.exon.36mer
mappa.mm9.exon.40mer	mappa.mm9.exon.40mer
mappa.mm9.exon.50mer	mappa.mm9.exon.50mer
mappa.mm9.exon.75mer	mappa.mm9.exon.75mer
mappa.mm9.intron.100mer	mappa.mm9.intron.100mer
mappa.mm9.intron.36mer	mappa.mm9.intron.36mer
mappa.mm9.intron.40mer	mappa.mm9.intron.40mer
mappa.mm9.intron.50mer	mappa.mm9.intron.50mer
mappa.mm9.intron.75mer	mappa.mm9.intron.75mer
mappa.mm9.nearest_gene.100mer	mappa.mm9.nearest_gene.100mer
mappa.mm9.nearest_gene.36mer	mappa.mm9.nearest_gene.36mer
mappa.mm9.nearest_gene.40mer	mappa.mm9.nearest_gene.40mer
mappa.mm9.nearest_gene.50mer	mappa.mm9.nearest_gene.50mer
mappa.mm9.nearest_gene.75mer	mappa.mm9.nearest_gene.75mer
mappa.mm9.nearest_tss.100mer	mappa.mm9.nearest_tss.100mer
mappa.mm9.nearest_tss.36mer	mappa.mm9.nearest_tss.36mer
mappa.mm9.nearest_tss.40mer	mappa.mm9.nearest_tss.40mer
mappa.mm9.nearest_tss.50mer	mappa.mm9.nearest_tss.50mer
mappa.mm9.nearest_tss.75mer	mappa.mm9.nearest_tss.75mer
ChIP-seq Peaks for the E2F4 Transcription Factor	peaks_E2F4
ChIP-seq Peaks for the Histone Modification H3K4me3 in GM12878	peaks_H3K4me3_GM12878
DTSS Spline adjustment	spline.log_dtss.90ENCODE
tss.danRer10 TSS locations	tss.danRer10
tss.dm3 TSS locations	tss.dm3
tss.dm6 TSS locations	tss.dm6
tss.hg19 TSS locations	tss.hg19
tss.hg38 TSS locations	tss.hg38
tss.mm10 TSS locations	tss.mm10
tss.mm9 TSS locations	tss.mm9
tss.rn4 TSS locations	tss.rn4
tss.rn5 TSS locations	tss.rn5
tss.rn6 TSS locations	tss.rn6