htSeqTools

DOI: 10.18129/B9.bioc.htSeqTools    

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

Quality Control, Visualization and Processing for High-Throughput Sequencing data

Bioconductor version: Release (3.7)

We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.

Author: Evarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar Flores, David Rossell

Maintainer: Oscar Reina <oscar.reina at irbbarcelona.org>

Citation (from within R, enter citation("htSeqTools")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("htSeqTools")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("htSeqTools")

 

PDF R Script Manual for the htSeqTools library
PDF   Reference Manual
Text   NEWS

Details

biocViews QualityControl, Sequencing, Software
Version 1.28.3
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License GPL (>=2)
Depends R (>= 2.12.2), methods, BiocGenerics(>= 0.1.0), Biobase, S4Vectors, IRanges, methods, MASS, BSgenome, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.11)
Imports
LinkingTo
Suggests
SystemRequirements
Enhances parallel, multicore
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 htSeqTools_1.28.3.tar.gz
Windows Binary htSeqTools_1.28.3.zip
Mac OS X 10.11 (El Capitan) htSeqTools_1.28.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/htSeqTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/htSeqTools
Package Short Url http://bioconductor.org/packages/htSeqTools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

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