htSeqTools

DOI: 10.18129/B9.bioc.htSeqTools    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see htSeqTools.

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

Bioconductor version: 3.8

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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("htSeqTools")

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("htSeqTools")

 

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

Details

biocViews QualityControl, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 2.9 (R-2.14) (7.5 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
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Build Report  

Package Archives

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

Source Package htSeqTools_1.30.0.tar.gz
Windows Binary htSeqTools_1.30.0.zip
Mac OS X 10.11 (El Capitan) htSeqTools_1.30.0.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/
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