recipe bioconductor-edaseq

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).

Homepage:https://bioconductor.org/packages/3.8/bioc/html/EDASeq.html License:Artistic-2.0 Recipe:/bioconductor-edaseq/meta.yaml Links:biotools: edaseq

package bioconductor-edaseq

Versions:

2.16.0-0, 2.14.1-0, 2.12.0-0, 2.10.0-0, 2.8.0-0

Depends:

• bioconductor-annotationdbi >=1.44.0,<1.45.0
• bioconductor-aroma.light >=3.12.0,<3.13.0
• bioconductor-biobase >=2.42.0,<2.43.0
• bioconductor-biocgenerics >=0.28.0,<0.29.0
• bioconductor-biomart >=2.38.0,<2.39.0
• bioconductor-biostrings >=2.50.0,<2.51.0
• bioconductor-deseq >=1.34.0,<1.35.0
• bioconductor-genomicfeatures >=1.34.0,<1.35.0
• bioconductor-genomicranges >=1.34.0,<1.35.0
• bioconductor-iranges >=2.16.0,<2.17.0
• bioconductor-rsamtools >=1.34.0,<1.35.0
• bioconductor-shortread >=1.40.0,<1.41.0
• r-base >=3.5.1,<3.5.2.0a0

Required By:

• bioconductor-tcgabiolinks
• bioconductor-metaseqr
• bioconductor-damirseq
• bioconductor-ruvseq
• bioconductor-consensusde
• bioconductor-enrichmentbrowser

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-edaseq

and update with:

conda update bioconductor-edaseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-edaseq:<tag>

(see bioconductor-edaseq/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-edaseq/README.html)