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QuasR

Quantify and Annotate Short Reads in R


Bioconductor version: Release (3.18)

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], Adam Alexander Thil SMITH [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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QuasR")

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

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.42.1
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-2
Depends R (>= 4.3), 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
System Requirements GNU make
URL
See More
Suggests Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat
Linking To Rhtslib(>= 1.99.1)
Enhances
Depends On Me
Imports Me SingleMoleculeFootprinting
Suggests Me eisaR
Links To Me
Build Report Build Report

Package Archives

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

Source Package QuasR_1.42.1.tar.gz
Windows Binary QuasR_1.42.1.zip
macOS Binary (x86_64) QuasR_1.42.1.tgz
macOS Binary (arm64) QuasR_1.42.1.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
Old Source Packages for BioC 3.18 Source Archive