recipe bioconductor-pram

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/pram.html

License

GPL (>= 3)

Recipe

/bioconductor-pram/meta.yaml

package bioconductor-pram

Versions

1.0.0-1

Depends

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-genomeinfodb >=1.20.0,<1.21.0

• bioconductor-genomicalignments >=1.20.0,<1.21.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-rsamtools >=2.0.0,<2.1.0

• bioconductor-rtracklayer >=1.44.0,<1.45.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• r-base >=3.6,<3.7.0a0

• r-data.table >=1.11.8

Required By

Installation

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

conda install bioconductor-pram

and update with:

conda update bioconductor-pram

or use the docker container:

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

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