triform

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 triform.

Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data


Bioconductor version: 3.10

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

Author: Karl Kornacker Developer [aut], Tony Handstad Developer [aut, cre]

Maintainer: Thomas Carroll <tc.infomatics at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("triform")

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("triform")
Triform users guide PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, Sequencing, Software
Version 1.28.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-2
Depends R (>= 2.11.0), IRanges, yaml
Imports BiocGenerics, IRanges(>= 2.5.27), yaml
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Package Archives

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

Source Package triform_1.28.0.tar.gz
Windows Binary triform_1.28.0.zip
Mac OS X 10.11 (El Capitan) triform_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/triform
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/triform
Bioc Package Browser https://code.bioconductor.org/browse/triform/
Package Short Url https://bioconductor.org/packages/triform/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive