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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 (3.3)

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.tan09 at>

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HTML Transcription factor binding site (TFBS) analysis with the TFBSTools package
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biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription
Version 1.9.6
In Bioconductor since BioC 2.13 (R-3.0) (2 years)
License GPL-2
Depends R (>= 3.2.2)
Imports Biobase(>= 2.28), Biostrings(>= 2.36.4), 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(>= 1.7.3), GenomicRanges(>= 1.20.6), gtools (>= 3.5.0), grid, IRanges(>= 2.2.7), methods, RSQLite (>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.6.5), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3), XVector(>= 0.8.0)
Suggests BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), RUnit (>= 0.4.29)
Depends On Me
Imports Me MatrixRider
Suggests Me
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