recipe bioconductor-mmappr2

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Homepage:

https://bioconductor.org/packages/3.17/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:

1.14.0-0,  1.8.0-0,  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:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-ensemblvep:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gmapr:

>=1.42.0,<1.43.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends bioconductor-varianttools:

>=1.42.0,<1.43.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-magrittr:

depends r-stringr:

depends r-tidyr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-mmappr2

and update with::

   mamba update bioconductor-mmappr2

To create a new environment, run:

mamba create --name myenvname bioconductor-mmappr2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-mmappr2/tags`_ for valid values for ``<tag>``)

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