ArrayExpressHTS

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ArrayExpressHTS.

ArrayExpress High Throughput Sequencing Processing Pipeline

DOI: 10.18129/B9.bioc.ArrayExpressHTS

Bioconductor version: 3.6

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>

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

Installation

To install this package, start R (version "3.4") and enter:


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

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("ArrayExpressHTS")

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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews RNASeq, Sequencing, Software

Version 1.28.0

In Bioconductor since BioC 2.8 (R-2.13) (13 years)

License Artistic License 2.0

Depends sampling, Rsamtools(>= 1.19.36), snow

Imports Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops

System Requirements

URL

Suggests

Linking To Rsamtools

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package ArrayExpressHTS_1.28.0.tar.gz

Windows Binary

Mac OS X 10.11 (El Capitan) ArrayExpressHTS_1.28.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/ArrayExpressHTS

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ArrayExpressHTS

Package Short Url https://bioconductor.org/packages/ArrayExpressHTS/

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Old Source Packages for BioC 3.6 Source Archive