QuasR

DOI: 10.18129/B9.bioc.QuasR  

This is the development version of QuasR; for the stable release version, see QuasR.

Quantify and Annotate Short Reads in R

Bioconductor version: Development (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 fmi.ch>

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews	Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	1.43.2
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 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, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi
LinkingTo	Rhtslib(>= 1.99.1)
Suggests	Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat
SystemRequirements	GNU make
Enhances
URL	https://bioconductor.org/packages/QuasR
BugReports	https://github.com/fmicompbio/QuasR/issues
Depends On Me
Imports Me	SingleMoleculeFootprinting
Suggests Me	eisaR
Links To Me
Build Report

Package Archives

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

Source Package	QuasR_1.43.2.tar.gz
Windows Binary	QuasR_1.43.2.zip
macOS Binary (x86_64)	QuasR_1.43.2.tgz
macOS Binary (arm64)
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