ArrayExpressHTS

DOI: 10.18129/B9.bioc.ArrayExpressHTS    

This package is for version 3.11 of Bioconductor; for the 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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	ImmunoOncology, RNASeq, Sequencing, Software
Version	1.38.0
In Bioconductor since	BioC 2.8 (R-2.13) (9.5 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
LinkingTo	Rhtslib(>= 1.15.3)
Suggests
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/ArrayExpressHTS/
Package Downloads Report	Download Stats