DOI: 10.18129/B9.bioc.QuasR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see QuasR.

Quantify and Annotate Short Reads in R

Bioconductor version: 3.9

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, Charlotte Soneson, Dimos Gaiditzis and Michael Stadler

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

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


To install this package, start R (version "3.6") and enter:

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


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


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biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.24.2
In Bioconductor since BioC 2.12 (R-3.0) (6.5 years)
License GPL-2
Depends R (>= 3.6), parallel, GenomicRanges(>= 1.13.3), Rbowtie
Imports methods, grDevices, graphics, utils, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools(>= 1.99.1), GenomicFeatures(>= 1.17.13), ShortRead(>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi
LinkingTo Rhtslib(>= 1.15.3)
Suggests Gviz, BiocStyle, knitr, rmarkdown, covr, testthat
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package QuasR_1.24.2.tar.gz
Windows Binary QuasR_1.24.2.zip
Mac OS X 10.11 (El Capitan) QuasR_1.24.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/QuasR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QuasR
Package Short Url https://bioconductor.org/packages/QuasR/
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