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DEScan2

This is the development version of DEScan2; for the stable release version, see DEScan2.

Differential Enrichment Scan 2

Bioconductor version: Development (3.18)

Integrated peak and differential caller, specifically designed for broad epigenomic signals.

Author: Dario Righelli [aut, cre], John Koberstein [aut], Bruce Gomes [aut], Nancy Zhang [aut], Claudia Angelini [aut], Lucia Peixoto [aut], Davide Risso [aut]

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Citation (from within R, enter citation("DEScan2")):

Installation

To install this package, start R (version "4.3") and enter: 

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

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

BiocManager::install("DEScan2")

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("DEScan2")
DEScan2 Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, Epigenetics, ImmunoOncology, PeakDetection, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 3.5), GenomicRanges
Imports BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors(>= 0.23.19), SummarizedExperiment, tools, utils
Linking To Rcpp, RcppArmadillo
Suggests BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod
System Requirements
Enhances
URL
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Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package DEScan2_1.21.0.tar.gz
Windows Binary DEScan2_1.21.0.zip (64-bit only)
macOS Binary (x86_64) DEScan2_1.21.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DEScan2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEScan2
Bioc Package Browser https://code.bioconductor.org/browse/DEScan2/
Package Short Url https://bioconductor.org/packages/DEScan2/
Package Downloads Report Download Stats