betterChromVAR
This is the released version of betterChromVAR; for the devel version, see betterChromVAR.
Improved ChromVAR (Chromatin Variation Across Regions)
Bioconductor version: Release (3.23)
A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.
Author: Pierre-Luc Germain [aut, cre] 
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("betterChromVAR")):Pierre-Luc Germain. betterChromVAR: Improved ChromVAR (Chromatin Variation Across Regions). doi:10.18129/B9.bioc.betterChromVAR, R package version 1.0.3, https://bioconductor.org/packages/betterChromVAR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("betterChromVAR")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("betterChromVAR")| Introduction to betterChromVAR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Epigenetics, Normalization, Sequencing, Software |
| Version | 1.0.3 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL (>= 3) |
| Depends | SummarizedExperiment |
| Imports | BiocParallel, Biostrings, GenomicRanges, IRanges, Matrix, matrixStats, methods, S4Vectors, stats |
| System Requirements | |
| URL | https://github.com/plger/betterChromVAR |
| Bug Reports | https://github.com/plger/betterChromVAR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, sessioninfo, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | betterChromVAR_1.0.3.tar.gz |
| Windows Binary (x86_64) | betterChromVAR_1.0.3.zip |
| macOS Binary (big-sur-x86_64) | betterChromVAR_1.0.3.tgz |
| macOS Binary (sonoma-arm64) | betterChromVAR_1.0.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/betterChromVAR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/betterChromVAR |
| Package Short Url | https://bioconductor.org/packages/betterChromVAR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |