ArrayExpressHTS

This package is for version 3.11 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


Bioconductor version: 3.11

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 "4.0") 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

Details

biocViews ImmunoOncology, RNASeq, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License Artistic License 2.0
Depends sampling, Rsamtools(>= 1.99.0), snow
Imports Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges(>= 2.13.11), R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops
System Requirements GNU make
URL
See More
Suggests
Linking To Rhtslib(>= 1.15.3)
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_1.38.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) ArrayExpressHTS_1.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ArrayExpressHTS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ArrayExpressHTS
Bioc Package Browser https://code.bioconductor.org/browse/ArrayExpressHTS/
Package Short Url https://bioconductor.org/packages/ArrayExpressHTS/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive