recipe bioconductor-mmappr2

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Homepage

https://bioconductor.org/packages/3.13/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

1.6.0-0,  1.4.0-0,  1.3.0-1,  1.3.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-ensemblvep >=1.34.0,<1.35.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-gmapr >=1.34.0,<1.35.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-variantannotation >=1.38.0,<1.39.0

• bioconductor-varianttools >=1.34.0,<1.35.0

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

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