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>

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