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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 (3.19)

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 "4.4") 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 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod
Linking To Rcpp, RcppArmadillo
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 DEScan2_1.23.0.tar.gz
Windows Binary DEScan2_1.23.0.zip
macOS Binary (x86_64) DEScan2_1.23.0.tgz
macOS Binary (arm64) DEScan2_1.23.0.tgz
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