| Title: | Reference data for GenomicDistributions package |
|---|---|
| Description: | This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10. |
| Authors: | Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan C. Sheffield [ctb] |
| Maintainer: | Kristyna Kupkova <[email protected]> |
| License: | BSD_2_clause + file LICENSE |
| Version: | 1.20.0 |
| Built: | 2026-10-10 11:15:07 UTC |
| Source: | https://github.com/bioc/GenomicDistributionsData |
Checks to make sure a package object is installed, and if so, returns it. If the library is not installed, it issues a warning and returns NULL.
.requireAndReturn(BSgenomeString).requireAndReturn(BSgenomeString)
BSgenomeString |
A BSgenome compatible genome string. |
A BSgenome object if installed.
Build chromosome sizes object
buildChromSizes(assembly)buildChromSizes(assembly)
assembly |
string, reference assembly identifier to chromosome sizes for |
named int, sizes of chromosome with respective names
## Not run: buildChromSizes("hg19") ## End(Not run)## Not run: buildChromSizes("hg19") ## End(Not run)
Build gene models
buildGeneModels(refAssembly)buildGeneModels(refAssembly)
refAssembly |
string, reference assembly identifier to build gene model for |
a list of four GRanges objects: genesGR, exonsGR, threeUTRGR, fiveUTRGR
## Not run: hg19models = buildGeneModels("hg19") ## End(Not run)## Not run: hg19models = buildGeneModels("hg19") ## End(Not run)
Build open signal matrix
buildOpenSignalMatrix(assembly)buildOpenSignalMatrix(assembly)
assembly |
string, reference assembly identifier to build gene model for |
data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values
## Not run: buildOpenSignalMatrix("hg19") ## End(Not run)## Not run: buildOpenSignalMatrix("hg19") ## End(Not run)
Build TSS
buildTSS(assembly)buildTSS(assembly)
assembly |
string, reference assembly identifier to TSS for |
GRanges object that consists of transcription start sites locations
## Not run: tss = buildTSS("hg19") ## End(Not run)## Not run: tss = buildTSS("hg19") ## End(Not run)
Table the maps cell types to tissues and groups
data.table with 3 columns (cellType, tissue and group) and 74 rows (one per cellType)
self-curated dataset
A dataset containing chromosome sizes for Homo sapiens hg19 genome assembly
chromSizes_hg19(metadata=FALSE)chromSizes_hg19(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A vector of lengths
BSgenome.Hsapiens.UCSC.hg19 package
hg19c = chromSizes_hg19()hg19c = chromSizes_hg19()
A dataset containing chromosome sizes for Homo sapiens hg38 genome assembly
chromSizes_hg38(metadata=FALSE)chromSizes_hg38(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A vector of lengths
BSgenome.Hsapiens.UCSC.hg38 package
hg38c = chromSizes_hg38()hg38c = chromSizes_hg38()
A dataset containing chromosome sizes for Mus musculus mm10 genome assembly
chromSizes_mm10(metadata=FALSE)chromSizes_mm10(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A vector of lengths
BSgenome.MMusculus.UCSC.mm10 package
mm10c = chromSizes_mm10()mm10c = chromSizes_mm10()
A dataset containing chromosome sizes for Mus musculus mm9 genome assembly
chromSizes_mm9(metadata=FALSE)chromSizes_mm9(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A vector of lengths
BSgenome.MMusculus.UCSC.mm9 package
mm9c = chromSizes_mm9()mm9c = chromSizes_mm9()
A dataset containing gene models for Homo sapiens hg19 genome assembly
geneModels_hg19(metadata=FALSE)geneModels_hg19(metadata=FALSE)
metadata |
|
A list of two GRanges objects, with genes and exons locations
A list with two GRanges objects.
EnsDb.Hsapiens.v75 package
hg19GeneModels = geneModels_hg19()hg19GeneModels = geneModels_hg19()
A dataset containing gene models for Homo sapiens hg38 genome assembly
geneModels_hg38(metadata=FALSE)geneModels_hg38(metadata=FALSE)
metadata |
|
A list of two GRanges objects, with genes and exons locations
A list with two GRanges objects.
EnsDb.Hsapiens.v86 package
hg38GeneModels = geneModels_hg38()hg38GeneModels = geneModels_hg38()
A dataset containing gene models for Mus musculus mm10 genome assembly
geneModels_mm10(metadata=FALSE)geneModels_mm10(metadata=FALSE)
metadata |
|
A list of two GRanges objects, with genes and exons locations
A list with two GRanges objects.
EnsDb.Mmusculus.v79 package
mm10GeneModels = geneModels_mm10()mm10GeneModels = geneModels_mm10()
A dataset containing gene models for Mus musculus mm9 genome assembly
geneModels_mm9(metadata=FALSE)geneModels_mm9(metadata=FALSE)
metadata |
|
A list of two GRanges objects, with genes and exons locations
A list with two GRanges objects.
TxDb.Mmusculus.UCSC.mm9.knownGene package
mm9GeneModels = geneModels_mm9()mm9GeneModels = geneModels_mm9()
Data (hg19, hg38, mm9, mm10) for the GenomicDistributions package.
The vignette details how to access the data from ExperimentHub: browseVignettes("GenomicDistributionsData") Details on how the data files were created can be found under the R directory in utils.R and build.R
UCSC hg19, hg38, mm9, mm10 genome packages and ensembldb
## Not run: library(ExperimentHub) hub = ExperimentHub() q = query(hub, "GenomicDistributionsData") q[[1]] q[["EH3472"]] ## End(Not run)## Not run: library(ExperimentHub) hub = ExperimentHub() q = query(hub, "GenomicDistributionsData") q[[1]] q[["EH3472"]] ## End(Not run)
This function will let you use a simple character vector (e.g. 'hg19') to load and then return BSgenome objects. This lets you avoid having to use the more complex annotation for a complete BSgenome object (e.g. BSgenome.Hsapiens.UCSC.hg38.masked)
loadBSgenome(genomeBuild, masked = TRUE)loadBSgenome(genomeBuild, masked = TRUE)
genomeBuild |
One of 'hg19', 'hg38', 'mm10', 'mm9', or 'grch38' |
masked |
Should we used the masked version? Default:TRUE |
a BSgenome object according to the specified genome assembly
## Not run: bsg = loadBSgenome('hg19') ## End(Not run)## Not run: bsg = loadBSgenome('hg19') ## End(Not run)
Load selected EnsDb library
loadEnsDb(genomeBuild)loadEnsDb(genomeBuild)
genomeBuild |
string, genome identifier |
loaded library
## Not run: loadEnsDb("hg19") ## End(Not run)## Not run: loadEnsDb("hg19") ## End(Not run)
Load selected TxDb library
loadTxDb(genomeBuild)loadTxDb(genomeBuild)
genomeBuild |
string, genome identifier |
loaded library
## Not run: loadTxDb("hg19") ## End(Not run)## Not run: loadTxDb("hg19") ## End(Not run)
Preparation steps:
made a universe of regions by merging regions across cell types defined as opened in ENCODE
took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites
evaluated the signal above regions defined by previous step
performed quantile normalization
openSignalMatrix_hg19(metadata=FALSE)openSignalMatrix_hg19(metadata=FALSE)
metadata |
|
data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values.
A data.frame with hg19 open chromatin regions.
## Not run: hg19OpenSignal = openSignalMatrix_hg19() ## End(Not run)## Not run: hg19OpenSignal = openSignalMatrix_hg19() ## End(Not run)
Preparation steps:
made a universe of regions by merging regions across cell types defined as opened in ENCODE
took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites
evaluated the signal above regions defined by previous step
performed quantile normalization
openSignalMatrix_hg38(metadata=FALSE)openSignalMatrix_hg38(metadata=FALSE)
metadata |
|
data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values.
A data.frame with hg38 open chromatin regions.
## Not run: hg38OpenSignal = openSignalMatrix_hg38() ## End(Not run)## Not run: hg38OpenSignal = openSignalMatrix_hg38() ## End(Not run)
Preparation steps:
made a universe of regions by merging regions across cell types defined as opened in ENCODE
took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites
evaluated the signal above regions defined by previous step
performed quantile normalization
openSignalMatrix_mm10(metadata=FALSE)openSignalMatrix_mm10(metadata=FALSE)
metadata |
|
data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values.
A data.frame with mm10 open chromatin regions.
## Not run: mm10OpenSignal = openSignalMatrix_mm10() ## End(Not run)## Not run: mm10OpenSignal = openSignalMatrix_mm10() ## End(Not run)
A dataset containing Transcription Start Sites for Homo sapiens hg19 genome assembly
TSS_hg19(metadata=FALSE)TSS_hg19(metadata=FALSE)
metadata |
|
A GRanges object with Transcription Start Site locations
A GRanges object with hg19 TSS locations.
EnsDb.Hsapiens.v75 package
hg19TSS = TSS_hg19()hg19TSS = TSS_hg19()
A dataset containing Transcription Start Sites for the Homo sapiens hg38 genome assembly
TSS_hg38(metadata=FALSE)TSS_hg38(metadata=FALSE)
metadata |
|
A GRanges object with Transcription Start Site locations
A GRanges object with hg38 TSS locations.
EnsDb.Hsapiens.v86 package
hg38TSS = TSS_hg38()hg38TSS = TSS_hg38()
A dataset containing Transcription Start Sites for the Mus musculus mm10 genome assembly
TSS_mm10(metadata=FALSE)TSS_mm10(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A GRanges object with mm10 TSS locations.
EnsDb.Mmusculus.v79 package
mm10TSS = TSS_mm10()mm10TSS = TSS_mm10()
A dataset containing Transcription Start Sites for the Mus musculus mm9 genome assembly
TSS_mm9(metadata=FALSE)TSS_mm9(metadata=FALSE)
metadata |
|
A named vectors of lengths with one item per chromosome
A GRanges object with mm9 TSS locations.
TxDb.Mmusculus.UCSC.mm9.knownGene package
mm9TSS = TSS_mm9()mm9TSS = TSS_mm9()