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Bioconductor - TFBSTools (development version)

TFBSTools

This is the development version of TFBSTools; for the stable release version, see TFBSTools.

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 Details biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription Version 1.47.0 In Bioconductor since BioC 2.13 (R-3.0) (11.5 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), GenomeInfoDb(>= 1.6.1), 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 See More 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, spatzie Suggests Me enhancerHomologSearch, GRaNIE, MAGAR, pageRank, universalmotif, JASPAR2018, JASPAR2020, JASPAR2022, CAGEWorkflow, Signac Links To Me Build Report Build Report Package Archives

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

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