TFBSTools

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

Software Package for Transcription Factor Binding Site (TFBS) Analysis

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DOI: 10.18129/B9.bioc.TFBSTools

Bioconductor version: Release (3.22)

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Author: Ge Tan [aut, cre]

Maintainer: Ge Tan <ge_tan at live.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("TFBSTools")

Transcription factor binding site (TFBS) analysis with the "TFBSTools" package HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription

Version 1.48.0

In Bioconductor since BioC 2.13 (R-3.0) (12 years)

License GPL-2

Depends R (>= 3.2.2)

Imports Biobase(>= 2.28), Biostrings(>= 2.36.4), pwalign, BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools (>= 1.17.1), DirichletMultinomial(>= 1.10.0), Seqinfo, GenomicRanges(>= 1.20.6), gtools (>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite (>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3), XVector(>= 0.8.0), parallel

System Requirements

URL https://github.com/ge11232002/TFBSTools

Bug Reports https://github.com/ge11232002/TFBSTools/issues

Suggests BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown

Linking To

Enhances

Depends On Me

Imports Me ATACseqTFEA, chromVAR, esATAC, MatrixRider, MethReg, monaLisa, motifmatchr, motifStack, primirTSS

Suggests Me enhancerHomologSearch, GRaNIE, MAGAR, pageRank, universalmotif, JASPAR2018, JASPAR2020, JASPAR2022, CAGEWorkflow, Signac

Links To Me

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