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.
EDASeq
Exploratory Data Analysis and Normalization for RNA-Seq
Bioconductor version: 3.0
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:
source("http://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, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| 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) |
| LinkingTo | |
| Suggests | BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | metaseqR, RUVSeq |
| Imports Me | |
| Suggests Me | HTSFilter, oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | EDASeq_2.0.0.tar.gz |
| Windows Binary | EDASeq_2.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | EDASeq_2.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | EDASeq_2.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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