fp-tools-bio

Pre-release

This release is a pre-release and may not be stable for production use.

fp-tools — regulatory footprinting

Documentation · Output demo with ENCODE cancer cell lines · GUI demo · PyPI

fp-tools is a command-first toolkit for footprinting Tn5-based chromatin profiling data, including ATAC-seq, CUT&Tag, and related assays. It provides bias correction, motif analysis, replicate-aware comparisons, and single-cell footprint signatures. The GUI and YAML runner call the same commands.

Install

Choose one route:

Route	Best for	Start
Desktop app	Windows or Apple Silicon macOS	Download
Python package	Windows, macOS, or Linux with Python 3.11–3.13	`python -m pip install fp-tools-bio`
Container	Complete reproducible environment	`docker build -t fp-tools:latest https://github.com/oncologylab/fp-tools.git#main`

Python package example:

python -m pip install --pre fp-tools-bio
fp-tools-gui

Optional de novo motif tools are downloaded into a private, versioned cache on first use. Docker remains an optional reproducible backend.

Bulk ATAC-seq

bulk-footprinting runs from coordinate-sorted BAM/BAI files and matching peak BED files through the final interactive comparison report.

bulk-footprinting \
  --sample-table samples.tsv \
  --comparison-table comparisons.tsv \
  --genome hg38.fa.gz \
  --outdir project \
  --cores 8

The wrapper runs atac-correct, call-footprints, match-motifs, diff-footprints, and review-multi-comparisons. Each command can also be run directly. diff-footprints --comparison-axis regions compares matched genomic region sets within one sample or across biological replicates.

Optional FASTQ-to-BAM preparation is a separate prepare-atac command on the Linux CLI and in the Linux container. bulk-footprinting, the GUI, and native macOS/Windows installations start from BAM/BAI and peak BED files.

Single-cell ATAC-seq

sc-footprinting groups fragments, runs pseudobulk footprinting, and produces per-cell KNN footprint-signature heatmaps and UMAPs.

sc-footprinting \
  --fragments fragments.tsv.gz \
  --annotations cell_annotations.tsv \
  --h5ad embedding.h5ad \
  --group-by cell_type \
  --genome-sizes hg38.chrom.sizes \
  --genome hg38.fa.gz \
  --peaks merged_peaks.bed \
  --outdir project/single_cell

Main commands

Area	Commands
Core analysis	`atac-correct`, `call-footprints`, `match-motifs`, `diff-footprints`, `normalize-bigwig`
Linux preprocessing	`prepare-atac`
Workflows	`bulk-footprinting`, `sc-footprinting`, `run-yaml-workflow`, `fp-tools-gui`, `fp-tools-runtime`
Reports	`plot-aggregate`, `review-multi-comparisons`
De novo motifs	`discover-motifs`, `summarize-motifs`
Single-cell utilities	`pseudobulk-fragments`, `find-signature-fp`

Use <command> --help for complete options. Practical examples and the API reference are available in the documentation.

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fp-tools-bio 0.2.0rc9

Install

Bulk ATAC-seq

Single-cell ATAC-seq

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