recipe bioconductor-inpas

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Homepage

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

License

GPL (>= 2)

Recipe

/bioconductor-inpas/meta.yaml

Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites due to internal-priming.

package bioconductor-inpas

Versions

1.20.0-0,  1.18.0-0,  1.16.3-0,  1.14.1-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-cleanupdtseq >=1.26.0,<1.27.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-gviz >=1.32.0,<1.33.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-preprocesscore >=1.50.0,<1.51.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-depmixs4

• r-seqinr

Required By

Installation

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

conda install bioconductor-inpas

and update with:

conda update bioconductor-inpas

or use the docker container:

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

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