ArrayExpressHTS

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 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: 3.17

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 "4.3") 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

Reference Manual PDF

Details

biocViews ImmunoOncology, RNASeq, Sequencing, Software
Version 1.50.0
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
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Suggests
Linking To Rhtslib(>= 1.15.3)
Enhances
Depends On Me
Imports Me
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive