QuasR

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see QuasR.

Quantify and Annotate Short Reads in R


Bioconductor version: 3.8

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, Dimos Gaiditzis and Michael Stadler

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

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

Installation

To install this package, start R (version "3.5") 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 1.22.1
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-2
Depends parallel, GenomicRanges(>= 1.13.3), Rbowtie
Imports methods, grDevices, graphics, utils, zlibbioc, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools(>= 1.19.38), GenomicFeatures(>= 1.17.13), ShortRead(>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles
System Requirements
URL
See More
Suggests Gviz, RUnit, BiocStyle, knitr, rmarkdown
Linking To Rsamtools
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package QuasR_1.22.1.tar.gz
Windows Binary QuasR_1.22.1.zip
Mac OS X 10.11 (El Capitan) QuasR_1.22.1.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 3.8 Source Archive