recipe bioconductor-pram

Pooling RNA-seq datasets for assembling transcript models

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/pram.html

License:

GPL (>= 3)

Recipe:

/bioconductor-pram/meta.yaml

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.

package bioconductor-pram

Versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-data.table >=1.11.8

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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