TFARM

This is the released version of TFARM; for the devel version, see TFARM.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Transcription Factors Association Rules Miner

Bioconductor version: Release (3.23)

It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.

Author: Liuba Nausicaa Martino, Alice Parodi, Gaia Ceddia, Piercesare Secchi, Stefano Campaner, Marco Masseroli

Maintainer: Liuba Nausicaa Martino <liuban.martino at gmail.com>

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

Liuba Nausicaa Martino, Alice Parodi, Gaia Ceddia, Piercesare Secchi, Stefano Campaner, Marco Masseroli. TFARM: Transcription Factors Association Rules Miner. doi:10.18129/B9.bioc.TFARM, R package version 1.34.0, https://bioconductor.org/packages/TFARM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("TFARM")

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("TFARM")

Transcription Factor Association Rule Miner	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, Infrastructure, Software, StatisticalMethod, Transcription
Version	1.34.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots
System Requirements
URL

Suggests	BiocStyle, knitr, plyr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	TFARM_1.34.0.tar.gz
Windows Binary (x86_64)	TFARM_1.34.0.zip
macOS Binary (big-sur-x86_64)	TFARM_1.34.0.tgz
macOS Binary (sonoma-arm64)	TFARM_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TFARM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TFARM
Package Short Url	https://bioconductor.org/packages/TFARM/
Package Downloads Report	Download Stats