QuasR

DOI: 10.18129/B9.bioc.QuasR    

This is the development version of QuasR; to use it, please install the devel version of Bioconductor.

Quantify and Annotate Short Reads in R

Bioconductor version: Development (3.10)

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, Charlotte Soneson, 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 "3.6") and enter:

if (!requireNamespace("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

Details

biocViews Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.25.2
In Bioconductor since BioC 2.12 (R-3.0) (6 years)
License GPL-2
Depends R (>= 3.6), parallel, GenomicRanges(>= 1.13.3), Rbowtie
Imports methods, grDevices, graphics, utils, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools(>= 1.99.1), GenomicFeatures(>= 1.17.13), ShortRead(>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi
LinkingTo Rhtslib(>= 1.15.3)
Suggests Gviz, BiocStyle, knitr, rmarkdown, covr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package QuasR_1.25.2.tar.gz
Windows Binary QuasR_1.25.2.zip
Mac OS X 10.11 (El Capitan) QuasR_1.25.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/QuasR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QuasR
Package Short Url http://bioconductor.org/packages/QuasR/
Package Downloads Report Download Stats

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