MMAPPR2

DOI: 10.18129/B9.bioc.MMAPPR2    

This is the development version of MMAPPR2; to use it, please install the devel version of Bioconductor.

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Bioconductor version: Development (3.10)

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.

Author: Kyle Johnsen [aut], Nathaniel Jenkins [aut], Jonathon Hill [cre]

Maintainer: Jonathon Hill <jhill at byu.edu>

Citation (from within R, enter citation("MMAPPR2")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MMAPPR2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MMAPPR2")

 

HTML R Script An Introduction to MMAPPR2
PDF   Reference Manual
Text   NEWS

Details

biocViews DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version 0.99.13
In Bioconductor since BioC 3.10 (R-3.6)
License GPL-3
Depends R (>= 3.6.0)
Imports ensemblVEP(>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils
LinkingTo
Suggests testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
SystemRequirements Ensembl VEP
Enhances
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/ https://github.com/kjohnsen/MMAPPR2
BugReports https://github.com/kjohnsen/MMAPPR2/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MMAPPR2_0.99.13.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) MMAPPR2_0.99.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/MMAPPR2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MMAPPR2
Package Short Url http://bioconductor.org/packages/MMAPPR2/
Package Downloads Report Download Stats

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