- recipe bioconductor-mmappr2
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
- Homepage
https://bioconductor.org/packages/3.14/bioc/html/MMAPPR2.html
- License
GPL-3
- Recipe
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
1.8.0-0
,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
>=2.54.0,<2.55.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-ensemblvep
>=1.36.0,<1.37.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-gmapr
>=1.36.0,<1.37.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-variantannotation
>=1.40.0,<1.41.0
bioconductor-varianttools
>=1.36.0,<1.37.0
r-base
>=4.1,<4.2.0a0
- 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¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-mmappr2/README.html)