DEScan2

DOI: 10.18129/B9.bioc.DEScan2    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DEScan2.

Differential Enrichment Scan 2

Bioconductor version: 3.8

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 "3.5") and enter:

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

 

HTML R Script DEScan2 Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, Epigenetics, ImmunoOncology, PeakDetection, Sequencing, Software
Version 1.2.1
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
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, SummarizedExperiment, tools, utils
LinkingTo Rcpp, RcppArmadillo
Suggests BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DEScan2_1.2.1.tar.gz
Windows Binary DEScan2_1.2.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DEScan2_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEScan2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEScan2
Package Short Url http://bioconductor.org/packages/DEScan2/
Package Downloads Report Download Stats

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