ArrayExpressHTS

ArrayExpress High Throughput Sequencing Processing Pipeline

Bioconductor version: 2.8

RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets

Author: Angela Goncalves, Andrew Tikhonov

Maintainer: Angela Goncalves <filimon at ebi.ac.uk>, Andrew Tikhonov <andrew at ebi.ac.uk>

To install this package, start R and enter:

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

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

    citation("ArrayExpressHTS")

Documentation

PDF R Script ArrayExpressHTS: RNA-Seq Pipeline for transcription profiling experiments
PDF   Reference Manual

Details

biocViews RNAseq, Sequencing, HighThroughputSequencing
Depends sampling, Rsamtools(>= 1.3.32), snow
Imports Biobase, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils
Suggests
System Requirements
License Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version 1.2.0
Since Bioconductor 2.8 (R-2.13)

Package Downloads

Package Source ArrayExpressHTS_1.2.0.tar.gz
Windows Binary
MacOS 10.5 (Leopard) binary ArrayExpressHTS_1.2.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center