triform

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 triform.

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


Bioconductor version: 3.7

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 "3.5") 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 1.22.0
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
System Requirements
URL
See More
Suggests RUnit
Linking To
Enhances
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 triform_1.22.0.tar.gz
Windows Binary triform_1.22.0.zip
Mac OS X 10.11 (El Capitan) triform_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/triform
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/triform
Package Short Url https://bioconductor.org/packages/triform/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive