ArrayExpressHTS
This package is for version 3.10 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: 3.10
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("ArrayExpressHTS")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.36.0 |
| 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_1.36.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | ArrayExpressHTS_1.36.0.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 3.10 | Source Archive |