triform

DOI: 10.18129/B9.bioc.triform    

This package is for version 3.11 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: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Triform users guide
PDF		Reference Manual

Details

biocViews	ChIPSeq, Sequencing, Software
Version	1.29.0
In Bioconductor since	BioC 2.11 (R-2.15) (8 years)
License	GPL-2
Depends	R (>= 2.11.0), IRanges, yaml
Imports	BiocGenerics, IRanges(>= 2.5.27), yaml
LinkingTo
Suggests	RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	triform_1.29.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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