Package: GenomicDistributionsData 1.21.0

Kristyna Kupkova

GenomicDistributionsData: Reference data for GenomicDistributions package

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]

GenomicDistributionsData_1.21.0.tar.gz
GenomicDistributionsData_1.21.0.tar.gz(r-4.7-any)GenomicDistributionsData_1.21.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GenomicDistributionsData/json (API)

# Install 'GenomicDistributionsData' in R:

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

Bug tracker:https://github.com/databio/genomicdistributionsdata/issues

On BioConductor:GenomicDistributionsData-1.21.0(data/experiment 3.24)GenomicDistributionsData-1.20.0(data/experiment 3.23)

experimenthub experimentdata genome datapkg

5.19 score 3 stars 26 scripts 15 exports 87 dependencies

Last updated from:e024c0a658. Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: yes.

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

Target	Result	Time
bioc-checks	WARNING	174
linux-devel	NOTE	337
source / vignettes	OK	281
linux-release	NOTE	396

Exports:chromSizes_hg19 chromSizes_hg38 chromSizes_mm10 chromSizes_mm9 geneModels_hg19 geneModels_hg38 geneModels_mm10 geneModels_mm9 openSignalMatrix_hg19 openSignalMatrix_hg38 openSignalMatrix_mm10 TSS_hg19 TSS_hg38 TSS_mm10 TSS_mm9

Dependencies:AnnotationDbi AnnotationFilter AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr dplyr ensembldb ExperimentHub fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lambda.r lazyeval lifecycle magrittr matrixStats memoise mime openssl pillar pkgconfig png ProtGenerics purrr R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors Seqinfo snow stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML XVector yaml

Getting started with GenomicDistributionsData

Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2020-11-16
Started: 2020-07-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
Build chromosome sizes object	buildChromSizes
Build gene models	buildGeneModels
Build open signal matrix	buildOpenSignalMatrix
Build TSS	buildTSS
Table the maps cell types to tissues and groups	cellTypeMetadata
hg19 chromosome sizes	chromSizes_hg19
hg38 chromosome sizes	chromSizes_hg38
mm10 chromosome sizes	chromSizes_mm10
mm9 chromosome sizes	chromSizes_mm9
hg19 gene models	geneModels_hg19
hg38 gene models	geneModels_hg38
mm10 gene models	geneModels_mm10
mm9 gene models	geneModels_mm9
GenomicDIstributionsData	GenomicDistributionsData
Loads BSgenome objects from UCSC-style character vectors.	loadBSgenome
Load selected EnsDb library	loadEnsDb
Load selected TxDb library	loadTxDb
A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19	openSignalMatrix_hg19
A dataset containing open chromatin regions across all cell types defined by ENCODE for Homo sapiens hg38	openSignalMatrix_hg38
A dataset containing open chromatin regions across all cell types defined by ENCODE for Mus musculus mm10	openSignalMatrix_mm10
hg19 TSS locations	TSS_hg19
hg38 TSS locations	TSS_hg38
mm10 TSS locations	TSS_mm10
mm9 TSS locations	TSS_mm9