recipe bioconductor-prebs

Probe region expression estimation for RNA-seq data for improved microarray comparability

Homepage

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

License

Artistic-2.0

Recipe

/bioconductor-prebs/meta.yaml

Links

biotools: prebs

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

package bioconductor-prebs

Versions

1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0

Depends

• bioconductor-affy >=1.66.0,<1.67.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rpa >=1.44.0,<1.45.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

Required By

Installation

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

conda install bioconductor-prebs

and update with:

conda update bioconductor-prebs

or use the docker container:

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

(see bioconductor-prebs/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-prebs/README.html)