ArrayExpressHTS

This package is for version 3.14 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: 3.14

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 "4.1") 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 ImmunoOncology, RNASeq, Sequencing, Software

Version 1.44.0

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, 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

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_1.44.0.tar.gz

Windows Binary

macOS 10.13 (High Sierra) ArrayExpressHTS_1.44.0.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 3.14 Source Archive