EDASeq (original) (raw)
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, seeEDASeq.
Exploratory Data Analysis and Normalization for RNA-Seq
Bioconductor version: 2.12
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 and Sandrine Dudoit
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")
| R Script | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | |
|---|---|---|
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, HighThroughputSequencing, Preprocessing, QualityControl, RNAseq, Software |
|---|---|
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
| License | Artistic-2.0 |
| Depends | BiocGenerics(>= 0.1.3), Biobase(>= 2.15.1), ShortRead(>= 1.11.42), Rsamtools(>= 1.5.75), aroma.light |
| Imports | methods, graphics, BiocGenerics, IRanges(>= 1.13.9), DESeq |
| LinkingTo | |
| Suggests | yeastRNASeq, leeBamViews, edgeR, DESeq |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | HTSFilter, oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | EDASeq_1.6.0.tar.gz |
|---|---|
| Windows Binary | EDASeq_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | EDASeq_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/EDASeq/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/EDASeq/ |
| Package Downloads Report | Download Stats |