To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("EDASeq")
In most cases, you don't need to download the package archive at all.
Bioconductor version: 2.14
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")
):
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("EDASeq")
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 |
biocViews | DifferentialExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 2.9 (R-2.14) |
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 |
Suggests | yeastRNASeq, leeBamViews, edgeR, DESeq |
System Requirements | |
URL | |
Depends On Me | metaseqR |
Imports Me | |
Suggests Me | HTSFilter, oneChannelGUI |
Follow Installation instructions to use this package in your R session.
Package Source | EDASeq_1.10.0.tar.gz |
Windows Binary | EDASeq_1.10.0.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | EDASeq_1.10.0.tgz |
Mac OS X 10.9 (Mavericks) | EDASeq_1.10.0.tgz |
Browse/checkout source | (username/password: readonly) |
Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!