MMAPPR2
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MMAPPR2data.
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Bioconductor version: 3.19
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("MMAPPR2")):
Installation
To install this package, start R (version "4.4") 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
| Reference Manual |
Details
| biocViews | DNASeq, PooledScreens, RNASeq, Software, VariantDetection |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 |
| System Requirements | Ensembl VEP, Samtools |
| URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/ https://github.com/kjohnsen/MMAPPR2 |
| Bug Reports | https://github.com/kjohnsen/MMAPPR2/issues |
See More
| Suggests | testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | MMAPPR2_1.18.0.tgz |
| macOS Binary (arm64) | |
| 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 | https://bioconductor.org/packages/MMAPPR2/ |
| Package Downloads Report | Download Stats |