recipe bioconductor-edaseq

Exploratory Data Analysis and Normalization for RNA-Seq

Homepage

https://bioconductor.org/packages/3.11/bioc/html/EDASeq.html

License

Artistic-2.0

Recipe

/bioconductor-edaseq/meta.yaml

Links

biotools: 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).

package bioconductor-edaseq

Versions

2.22.0-0,  2.20.0-0,  2.18.0-1,  2.16.0-0,  2.14.1-0,  2.12.0-0,  2.10.0-0,  2.8.0-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-aroma.light >=3.18.0,<3.19.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biomart >=2.44.0,<2.45.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-deseq >=1.39.0,<1.40.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-shortread >=1.46.0,<1.47.0

• r-base >=4.0,<4.1.0a0

• r-biocmanager

Required By

• bioconductor-metaseqr2

• bioconductor-metaseqr

• bioconductor-damirseq

• bioconductor-consensusde

• bioconductor-tcgabiolinks

• bioconductor-ribosomeprofilingqc

• bioconductor-ruvseq

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)