To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("chromVAR")

In most cases, you don't need to download the package archive at all.

chromVAR

DOI: 10.18129/B9.bioc.chromVAR    

This is the development version of chromVAR; for the stable release version, see chromVAR.

Chromatin Variation Across Regions

Bioconductor version: Development (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("chromVAR")

Documentation

HTML R Script Introduction
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneRegulation, Sequencing, SingleCell, Software
Version 1.1.1
License MIT + file LICENSE
Depends R (>= 3.4)
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
Suggests Me
Build Report  

Package Archives

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

Source Package chromVAR_1.1.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) chromVAR_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/chromVAR
Package Short Url http://bioconductor.org/packages/chromVAR/
Package Downloads Report Download Stats

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