chromVAR
This is thereleased version of chromVAR; for the devel version, seechromVAR.
Chromatin Variation Across Regions
Bioconductor version: Release (3.22)
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("chromVAR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("chromVAR")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneRegulation,ImmunoOncology,Sequencing,SingleCell,Software |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| License | MIT + fileLICENSE |
| Depends | R (>= 3.5.0) |
| Imports | IRanges,Seqinfo,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 |
See More
| Suggests | JASPAR2016,BSgenome.Hsapiens.UCSC.hg19,readr,testthat,knitr,rmarkdown,pheatmap,motifmatchr |
| Linking To | Rcpp,RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Signac |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | chromVAR_1.32.0.tar.gz |
| Windows Binary (x86_64) | chromVAR_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | chromVAR_1.32.0.tgz |
| macOS Binary (arm64) | chromVAR_1.32.0.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 |