MMAPPR2

DOI: 10.18129/B9.bioc.MMAPPR2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MMAPPR2.

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
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, stringr, data.table
LinkingTo
Suggests	testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
SystemRequirements	Ensembl VEP, Samtools
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_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MMAPPR2
Source Repository (Developer Access)	git clone [email protected]:packages/MMAPPR2
Bioc Package Browser	https://code.bioconductor.org/browse/MMAPPR2/
Package Short Url	https://bioconductor.org/packages/MMAPPR2/
Package Downloads Report	Download Stats