DOI: 10.18129/B9.bioc.QuasR  

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

Quantify and Annotate Short Reads in R

Bioconductor version: 3.16

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

Author: Anita Lerch [aut], Charlotte Soneson [aut] , Dimos Gaidatzis [aut], Michael Stadler [aut, cre]

Maintainer: Michael Stadler <michael.stadler at fmi.ch>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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



HTML R Script An introduction to QuasR
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.12 (R-3.0) (10 years)
License GPL-2
Depends R (>= 4.1), parallel, GenomicRanges, Rbowtie
Imports methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools(>= 2.13.1), GenomicFeatures, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi
LinkingTo Rhtslib(>= 1.99.1)
Suggests Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat
SystemRequirements GNU make
Depends On Me
Imports Me SingleMoleculeFootprinting
Suggests Me eisaR
Links To Me
Build Report  

Package Archives

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

Source Package QuasR_1.38.0.tar.gz
Windows Binary QuasR_1.38.0.zip
macOS Binary (x86_64) QuasR_1.38.0.tgz
macOS Binary (arm64) QuasR_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QuasR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QuasR
Bioc Package Browser https://code.bioconductor.org/browse/QuasR/
Package Short Url https://bioconductor.org/packages/QuasR/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: