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>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("EDASeq")
To cite this package in a publication, start R and enter:
citation("EDASeq")
Documentation
| R Script | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | HighThroughputSequencing, RNAseq, Preprocessing, QualityControl, DifferentialExpression |
| Depends | Biobase, ShortRead(>= 1.11.42), Rsamtools(>= 1.5.75), aroma.light |
| Imports | methods, graphics, IRanges, DESeq |
| Suggests | yeastRNASeq, leeBamViews, edgeR, DESeq |
| System Requirements | |
| License | Artistic-2.0 |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | oneChannelGUI |
| Version | 1.0.0 |
| Since | Bioconductor 2.9 (R-2.14) |
Package Downloads
| Package Source | EDASeq_1.0.0.tar.gz |
| Windows Binary | EDASeq_1.0.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | EDASeq_1.0.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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