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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>

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

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")
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 1.43.4
In Bioconductor since BioC 2.12 (R-3.0) (11 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, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi
System Requirements GNU make
URL https://bioconductor.org/packages/QuasR
Bug Reports https://github.com/fmicompbio/QuasR/issues
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_1.43.4.tar.gz
Windows Binary QuasR_1.43.4.zip
macOS Binary (x86_64) QuasR_1.43.4.tgz
macOS Binary (arm64) QuasR_1.43.4.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