htSeqTools
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 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see htSeqTools.
Quality Control, Visualization and Processing for High-Throughput Sequencing data
Bioconductor version: 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("htSeqTools")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("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")| Manual for the htSeqTools library | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | QualityControl, Sequencing, Software |
| Version | 1.28.3 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 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 | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | parallel, multicore |
| 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 | 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 | https://bioconductor.org/packages/htSeqTools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |