chromVAR

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see chromVAR.

Chromatin Variation Across Regions

Bioconductor version: 3.18

Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

Author: Alicia Schep [aut, cre], Jason Buenrostro [ctb], Caleb Lareau [ctb], William Greenleaf [ths], Stanford University [cph]

Maintainer: Alicia Schep <aschep at gmail.com>

Citation (from within R, enter citation("chromVAR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("chromVAR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("chromVAR")

Introduction HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software

Version 1.24.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

License MIT + file LICENSE

Depends R (>= 3.5.0)

Imports IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome

System Requirements C++11

URL

Suggests JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me

Imports Me ATACCoGAPS

Suggests Me MOCHA, Signac

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chromVAR_1.24.0.tar.gz

Windows Binary chromVAR_1.24.0.zip

macOS Binary (x86_64) chromVAR_1.24.0.tgz

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/chromVAR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chromVAR

Bioc Package Browser https://code.bioconductor.org/browse/chromVAR/

Package Short Url https://bioconductor.org/packages/chromVAR/

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