Rmmquant
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rmmquant.
RNA-Seq multi-mapping Reads Quantification Tool
Bioconductor version: 3.9
RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.
Author: Zytnicki Matthias [aut, cre]
Maintainer: Zytnicki Matthias <matthias.zytnicki at inra.fr>
citation("Rmmquant")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rmmquant")
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("Rmmquant")| The Rmmquant package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, BiocStyle |
| System Requirements | C++11 |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rmmquant_1.2.0.tar.gz |
| Windows Binary | Rmmquant_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | Rmmquant_1.1.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rmmquant |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rmmquant |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rmmquant/ |
| Package Short Url | https://bioconductor.org/packages/Rmmquant/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |