EDASeq

DOI: 10.18129/B9.bioc.EDASeq    

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Release (3.7)

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:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("EDASeq")

Documentation

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

browseVignettes("EDASeq")

 

PDF R Script EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 2.14.1
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
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
Links To Me
Build Report  

Package Archives

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

Source Package EDASeq_2.14.1.tar.gz
Windows Binary EDASeq_2.14.1.zip
Mac OS X 10.11 (El Capitan) EDASeq_2.14.1.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
Old Source Packages for BioC 3.7 Source Archive

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