EDASeq

DOI: 10.18129/B9.bioc.EDASeq    

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

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Development (3.8)

Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

Author: Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Ludwig Geistlinger [ctb]

Maintainer: Davide Risso <risso.davide at gmail.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("EDASeq", version = "devel")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EDASeq")

 

HTML R Script zinbwave Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 2.15.3
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License Artistic-2.0
Depends Biobase(>= 2.15.1), ShortRead(>= 1.11.42)
Imports methods, graphics, BiocGenerics, IRanges(>= 1.13.9), DESeq, aroma.light, Rsamtools(>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges
LinkingTo
Suggests BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat
SystemRequirements
Enhances
URL https://github.com/drisso/EDASeq
BugReports https://github.com/drisso/EDASeq/issues
Depends On Me metaseqR, RUVSeq
Imports Me DaMiRseq, EnrichmentBrowser, TCGAbiolinks
Suggests Me DEScan2, HTSFilter
Build Report  

Package Archives

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

Source Package EDASeq_2.15.3.tar.gz
Windows Binary EDASeq_2.15.3.zip
Mac OS X 10.11 (El Capitan) EDASeq_2.15.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/EDASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EDASeq
Package Short Url http://bioconductor.org/packages/EDASeq/
Package Downloads Report Download Stats

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