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chromVAR

Chromatin Variation Across Regions

Bioconductor version: Release (3.17)

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

Details

biocViews GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software
Version 1.22.1
In Bioconductor since BioC 3.6 (R-3.4) (6 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
Linking To Rcpp, RcppArmadillo
Suggests JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr
System Requirements C++11
Enhances
URL
See More
Depends On Me
Imports Me ATACCoGAPS
Suggests Me MOCHA, Signac
Links To Me
Build Report  

Package Archives

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

Source Package chromVAR_1.22.1.tar.gz
Windows Binary chromVAR_1.22.1.zip
macOS Binary (x86_64) chromVAR_1.22.1.tgz
macOS Binary (arm64) chromVAR_1.22.1.tgz
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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive