TFBSTools
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see TFBSTools.
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Bioconductor version: 3.19
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("TFBSTools")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (11 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), CNEr(>= 1.4.0), 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 | ATACCoGAPS, ATACseqTFEA, MatrixRider, MethReg, chromVAR, esATAC, monaLisa, motifStack, motifmatchr, primirTSS, spatzie |
| Suggests Me | GRaNIE, MAGAR, enhancerHomologSearch, 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.
| Source Package | TFBSTools_1.42.0.tar.gz |
| Windows Binary (x86_64) | TFBSTools_1.42.0.zip |
| macOS Binary (x86_64) | TFBSTools_1.42.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/TFBSTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TFBSTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/TFBSTools/ |
| Package Short Url | https://bioconductor.org/packages/TFBSTools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |