QuasR

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see QuasR.

Quantify and Annotate Short Reads in R

Bioconductor version: 3.15

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")):

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software

Version 1.36.0

In Bioconductor since BioC 2.12 (R-3.0) (11 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, GenomicFeatures, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi

System Requirements GNU make

URL

Suggests Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat

Linking To Rhtslib

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_1.36.0.tar.gz

Windows Binary QuasR_1.36.0.zip

macOS Binary (x86_64) QuasR_1.36.0.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

Old Source Packages for BioC 3.15 Source Archive