recipe bioconductor-mmappr2

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Homepage

https://bioconductor.org/packages/3.11/bioc/html/MMAPPR2.html

License

GPL-3

Recipe

/bioconductor-mmappr2/meta.yaml

MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2 cross of forward genetic screens. Its predecessor is described in a paper published in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as a reference genome as input, identifies loci of high sequence disparity between the control and mutant RNA sequences, predicts variant effects using Ensembl's Variant Effect Predictor, and outputs a ranked list of candidate mutations.

package bioconductor-mmappr2

Versions

1.2.0-0,  1.0.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-ensemblvep >=1.30.0,<1.31.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-gmapr >=1.30.0,<1.31.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-variantannotation >=1.34.0,<1.35.0

• bioconductor-varianttools >=1.30.0,<1.31.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-dplyr

• r-magrittr

• r-stringr

• r-tidyr

Required By

Installation

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

conda install bioconductor-mmappr2

and update with:

conda update bioconductor-mmappr2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-mmappr2:<tag>

(see bioconductor-mmappr2/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-mmappr2/README.html)