To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EDASeq")

In most cases, you don't need to download the package archive at all.

EDASeq

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see EDASeq.

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: 3.2

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("https://bioconductor.org/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 EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data
PDF Reference Manual
Text NEWS

Details

biocViews DifferentialExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 2.4.1
In Bioconductor since BioC 2.9 (R-2.14) (4.5 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 EnrichmentBrowser, TCGAbiolinks
Suggests Me HTSFilter, oneChannelGUI
Build Report

Package Archives

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

Package Source EDASeq_2.4.1.tar.gz
Windows Binary EDASeq_2.4.1.zip
Mac OS X 10.6 (Snow Leopard) EDASeq_2.4.0.tgz
Mac OS X 10.9 (Mavericks) EDASeq_2.4.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/EDASeq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/EDASeq/
Package Downloads Report Download Stats

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