compEpiTools

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

Tools for computational epigenomics


Bioconductor version: Development (3.20)

Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]

Maintainer: Mattia Furlan <mattia.furlan at iit.it>

Citation (from within R, enter citation("compEpiTools")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("compEpiTools")

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("compEpiTools")
compEpiTools.pdf PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, GeneExpression, GenomeAnnotation, Sequencing, Software, Visualization
Version 1.39.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL
Depends R (>= 3.5.0), methods, topGO, GenomicRanges
Imports AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb
System Requirements
URL
See More
Suggests BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer
Linking To
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Depends On Me
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Package Archives

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

Source Package compEpiTools_1.39.0.tar.gz
Windows Binary compEpiTools_1.39.0.zip
macOS Binary (x86_64) compEpiTools_1.39.0.tgz
macOS Binary (arm64) compEpiTools_1.39.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/compEpiTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/compEpiTools
Bioc Package Browser https://code.bioconductor.org/browse/compEpiTools/
Package Short Url https://bioconductor.org/packages/compEpiTools/
Package Downloads Report Download Stats