# Bioconductor Tfbstools

TFBSTools is a package for the analysis and manipulation of transcription factor...

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-tfbstools -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-tfbstools -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-tfbstools -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-tfbstools -g -a gemini-cli -y`

## Description

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 c

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# TFBSTools

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

- **Version:** 1.50.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Imports:** Biobase, Biostrings, pwalign, BiocGenerics, BiocParallel, BSgenome, caTools, DirichletMultinomial, Seqinfo, GenomicRanges, gtools, IRanges, DBI, RSQLite, rtracklayer, seqLogo, S4Vectors, TFMPvalue, XML, XVector
- **Install:** `BiocManager::install("TFBSTools")`

## When to Use
- **Matrix Conversion**: Converting Position Frequency Matrices (PFMs) to Position Weight Matrices (PWMs) or Information Content Matrices (ICMs) using `toPWM` and `toICM`.
- **Motif Scanning**: Scanning nucleotide sequences or pairwise alignments for transcription factor binding sites using `searchSeq` or `searchAln`.
- **Database Querying**: Querying and retrieving matrix data from the JASPAR database using `getMatrixSet`.
- **Random Profile Generation**: Generating random profile matrices via permutation or Dirichlet multinomial mixture models using `permuteMatrix` and `rPWMDmm`.
- **Visualization**: Visualizing sequence logos for basic PWMs or Transcription Factor Flexible Models (TFFMs) using `seqLogo`.

## When NOT to Use
- For high-throughput scanning of thousands of large genomic regions, use `motifmatchr` instead, because `searchSeq` is optimized for targeted `DNAString` or `DNAStringSet` objects rather than massive `GRanges` peak sets.
- For de novo motif discovery without external dependencies, use `universalmotif` because `runMEME` requires the external MEME suite to be installed on the system.

## Data Requirements
- **Input Format**: `PFMatrix` objects, `DNAString` or `DNAStringSet` for sequences, and `Axt` objects for alignments.
- **Structure**: 4-row matrices representing A, C, G, T counts or probabilities.
- **Normalization State**: Raw position frequency counts for PFMs, which are then converted to log2 probability ratios for PWMs.

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/genomics/tfbstools/SKILL.md