EDASeq

DOI: 10.18129/B9.bioc.EDASeq    

Exploratory Data Analysis and Normalization for RNA-Seq

Bioconductor version: Release (3.6)

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>

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	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	2.12.0
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 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	DaMiRseq, EnrichmentBrowser, TCGAbiolinks
Suggests Me	HTSFilter, oneChannelGUI
Build Report

Package Archives

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

Source Package	EDASeq_2.12.0.tar.gz
Windows Binary	EDASeq_2.12.0.zip
Mac OS X 10.11 (El Capitan)	EDASeq_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EDASeq
Package Short Url	http://bioconductor.org/packages/EDASeq/
Package Downloads Report	Download Stats