QuasR

Quantify and Annotate Short Reads in R

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("QuasR")

To cite this package in a publication, start R and enter:

    citation("QuasR")

Documentation

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

Details

biocViews ChIPSeq, Genetics, MethylSeq, Preprocessing, RNASeq, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-2
Depends parallel, GenomicRanges(>= 1.13.3), Rbowtie
Imports methods, zlibbioc, BiocGenerics, IRanges, BiocInstaller, Biobase, Biostrings, GenomicRanges, BSgenome, Rsamtools(>= 1.13.1), GenomicFeatures, ShortRead(>= 1.19.1), GenomicAlignments
Suggests Rsamtools, rtracklayer, Gviz, RUnit, BiocStyle
System Requirements
URL
Depends On Me
Imports Me
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Package Downloads

Package Source QuasR_1.5.0.tar.gz
Windows Binary QuasR_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) QuasR_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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