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Quantify and Annotate Short Reads in R

Bioconductor version: Release (3.19)

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. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Author: Anita Lerch [aut], Adam Alexander Thil SMITH [aut] , Charlotte Soneson [aut] , Dimos Gaidatzis [aut], Michael Stadler [aut, cre]

Maintainer: Michael Stadler <michael.stadler at>

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


To install this package, start R (version "4.4") 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:

An introduction to QuasR HTML R Script
Reference Manual PDF


biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.44.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)
License GPL-2
Depends R (>= 4.4), parallel, GenomicRanges, Rbowtie
Imports methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools(>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi
System Requirements GNU make
Bug Reports
See More
Suggests Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat
Linking To Rhtslib(>= 1.99.1)
Depends On Me
Imports Me SingleMoleculeFootprinting
Suggests Me eisaR
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package QuasR_1.44.0.tar.gz
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macOS Binary (x86_64) QuasR_1.44.0.tgz
macOS Binary (arm64) QuasR_1.44.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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