Package: nullrangesData 1.19.0

Michael Love

nullrangesData: ExperimentHub datasets for the nullranges package

Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package.

Authors:Michael Love [aut, cre], Wancen Mu [aut], Eric Davis [aut], Mikhail Dozmorov [aut]

nullrangesData_1.19.0.tar.gz
nullrangesData_1.19.0.tar.gz(r-4.7-any)nullrangesData_1.19.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
nullrangesData/json (API)

# Install 'nullrangesData' in R:

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

Datasets:

sc_promoter - Chromium Single Cell Multiome ATAC + Gene Expression assay
sc_rna - Chromium Single Cell Multiome ATAC + Gene Expression assay

On BioConductor:nullrangesData-1.19.0(data/experiment 3.24)nullrangesData-1.18.0(data/experiment 3.23)

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

experimenthub homo_sapiens_data sequencingdata chipseqdata encode datapkg

3.45 score 14 scripts 3 exports 69 dependencies

Last updated from:051fe60c3c. Checks:1 WARNING, 3 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	157
linux-devel	OK	314
source / vignettes	OK	462
linux-release	OK	443

Exports:DHSA549Hg38 hg19_10kb_bins hg19_10kb_ctcfBoundBinPairs

Dependencies:abind AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr DelayedArray dplyr ExperimentHub fastmap filelock generics GenomicRanges glue httr httr2 InteractionSet IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 rappdirs Rcpp rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

nullrangesData package

Session information

Rendered fromnullrangesData.Rmdusingknitr::rmarkdown

Last update: 2023-02-03
Started: 2021-09-22

Help page	Topics
DNase hypersensitivity (DHS) peaks in A549 cell example data, lifted to hg38	DHSA549Hg38
10Kb bins from hg19 with GM12878 metadata annotation features	hg19_10kb_bins
CTCF-bound 10Kb paired genomic interactions	hg19_10kb_ctcfBoundBinPairs
ExperimentHub datasets for the nullranges package	nullrangesData
Chromium Single Cell Multiome ATAC + Gene Expression assay	sc_promoter
Chromium Single Cell Multiome ATAC + Gene Expression assay	sc_rna

Package: nullrangesData 1.19.0

nullrangesData: ExperimentHub datasets for the nullranges package

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)