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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("htSeqTools")
In most cases, you don't need to download the package archive at all.
htSeqTools
Quality Control, Visualization and Processing for High-Throughput Sequencing data
Bioconductor version: 2.14
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:
source("http://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")
| R Script | Manual for the htSeqTools library | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | QualityControl, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>=2) |
| Depends | R (>= 2.12.2), methods, BiocGenerics(>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges |
| Imports | |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | htSeqTools_1.10.0.tar.gz |
| Windows Binary | htSeqTools_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | htSeqTools_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | htSeqTools_1.10.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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