betterChromVAR
This is the development version of betterChromVAR; to use it, please install the devel version of Bioconductor.
Improved ChromVAR (Chromatin Variation Across Regions)
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | ATACSeq, Epigenetics, Normalization, Sequencing, Software |
| Version | 0.99.35 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | betterChromVAR_0.99.35.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | betterChromVAR_0.99.35.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/betterChromVAR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/betterChromVAR |
| Bioc Package Browser | https://code.bioconductor.org/browse/betterChromVAR/ |
| Package Short Url | https://bioconductor.org/packages/betterChromVAR/ |
| Package Downloads Report | Download Stats |