Package Recipe 'bioconductor-mmappr2'

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:

on bioconductor-biobase >=2.60.0,<2.61.0
on bioconductor-biocgenerics >=0.46.0,<0.47.0
on bioconductor-biocparallel >=1.34.0,<1.35.0
on bioconductor-ensemblvep >=1.42.0,<1.43.0
on bioconductor-genomeinfodb >=1.36.0,<1.37.0
on bioconductor-genomicranges >=1.52.0,<1.53.0
on bioconductor-gmapr >=1.42.0,<1.43.0
on bioconductor-iranges >=2.34.0,<2.35.0
on bioconductor-rsamtools >=2.16.0,<2.17.0
on bioconductor-s4vectors >=0.38.0,<0.39.0
on bioconductor-variantannotation >=1.46.0,<1.47.0
on bioconductor-varianttools >=1.42.0,<1.43.0
on r-base >=4.3,<4.4.0a0
on r-data.table
on r-dplyr
on r-magrittr
on r-stringr
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-mmappr2

to add into an existing workspace instead, run:

pixi add bioconductor-mmappr2

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-mmappr2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mmappr2

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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)