chromVAR

DOI: 10.18129/B9.bioc.chromVAR  

Chromatin Variation Across Regions

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software
Version	1.20.2
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo	Rcpp, RcppArmadillo
Suggests	JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr
SystemRequirements	C++11
Enhances
URL
Depends On Me
Imports Me	ATACCoGAPS
Suggests Me	Signac
Links To Me
Build Report

Package Archives

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

Source Package	chromVAR_1.20.2.tar.gz
Windows Binary	chromVAR_1.20.2.zip (64-bit only)
macOS Binary (x86_64)	chromVAR_1.20.2.tgz
macOS Binary (arm64)	chromVAR_1.20.2.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 3.16	Source Archive