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 2.9 of Bioconductor; for the stable, up-to-date release version, see EDASeq.
Exploratory Data Analysis and Normalization for RNA-Seq
Bioconductor version: 2.9
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")
| EDASeq.pdf | ||
| Reference Manual |
Details
| biocViews | DifferentialExpression, HighThroughputSequencing, Preprocessing, QualityControl, RNAseq, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
| License | Artistic-2.0 |
| Depends | Biobase, ShortRead(>= 1.11.42), Rsamtools(>= 1.5.75), aroma.light |
| Imports | methods, graphics, IRanges, DESeq |
| LinkingTo | |
| Suggests | yeastRNASeq, leeBamViews, edgeR, DESeq |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | EDASeq_1.0.0.tar.gz |
| Windows Binary | EDASeq_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/EDASeq/tree/release-2.9 |
| Package Short Url | http://bioconductor.org/packages/EDASeq/ |
| Package Downloads Report | Download Stats |
Documentation »
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