fp-tools-bio

_{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.

Metadata

Release files for fp-tools-bio 0.2.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for fp-tools-bio 0.2.1
File	Size	Uploaded
fp_tools_bio-0.2.1.tar.gz	1.5 MB	Aug 26, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for fp-tools-bio 0.2.1
File	Interpreter	ABI	Platform	Reset
fp_tools_bio-0.2.1-cp313-cp313-win_amd64.whl 1.7 MB Aug 26, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl 3.0 MB Aug 26, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.17+ x86-64	Details
fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl 3.0 MB Aug 26, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ ARM64, Linux glibc 2.28+ ARM64	Details
fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_x86_64.whl 1.7 MB Aug 26, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ x86-64	Details
fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_arm64.whl 1.7 MB Aug 26, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
fp_tools_bio-0.2.1-cp312-cp312-win_amd64.whl 1.7 MB Aug 26, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl 3.0 MB Aug 26, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.17+ x86-64	Details
fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl 3.0 MB Aug 26, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.28+ ARM64, Linux glibc 2.17+ ARM64	Details
fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_x86_64.whl 1.7 MB Aug 26, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ x86-64	Details
fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_arm64.whl 1.7 MB Aug 26, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
fp_tools_bio-0.2.1-cp311-cp311-win_amd64.whl 1.7 MB Aug 26, 2026	CPython 3.11	CPython 3.11	Windows x86-64	Details
fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl 3.0 MB Aug 26, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.28+ x86-64, Linux glibc 2.17+ x86-64	Details
fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl 3.0 MB Aug 26, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.28+ ARM64, Linux glibc 2.17+ ARM64	Details
fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_x86_64.whl 1.7 MB Aug 26, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ x86-64	Details
fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_arm64.whl 1.7 MB Aug 26, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details

Total release size: 34.8 MB

Release files / fp_tools_bio-0.2.1.tar.gz

Download URL	fp_tools_bio-0.2.1.tar.gz
Size	1.5 MB
Tags	Source
SHA-256 checksum How to use checksums	`9238dde08c90465d72b2d3783c434cb1901319012a57980c7ce5f3e6c728fdc7`
BLAKE2b-256 checksum How to use checksums	`61b84aafae0c208777e74203c3cc6b381cf0b1bdb7c11f9cc54b5552046b7bd4`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp313-cp313-win_amd64.whl

Download URL	fp_tools_bio-0.2.1-cp313-cp313-win_amd64.whl
Size	1.7 MB
Tags	CPython 3.13 Windows x86-64
SHA-256 checksum How to use checksums	`517d04ddfe3ddfe4cc91943c073fb530edfcd2ed3a7227800218228cfa8f09a5`
BLAKE2b-256 checksum How to use checksums	`9812e6b12f33f8658b2bf7ddb8cfb6462ddc1bf1db06900df88df86bc188b86c`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
Size	3.0 MB
Tags	CPython 3.13 Linux glibc 2.17+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`8ce2fbda102da96fdd74b81cfc6671c8acb938b365fea47dfaff6a49dd4c0db7`
BLAKE2b-256 checksum How to use checksums	`e86d85ecb187fe7f0220975585b791b328e78811d597e5420f71bbcccb6e9a83`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl

Download URL	fp_tools_bio-0.2.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
Size	3.0 MB
Tags	CPython 3.13 Linux glibc 2.17+ ARM64 Linux glibc 2.28+ ARM64
SHA-256 checksum How to use checksums	`2c13a9fc3e5b7a76054e904ec626e885ab06a80f3801e64dbaf7c49069008917`
BLAKE2b-256 checksum How to use checksums	`979f707f2eac5eca93600cf7b8a44c3fc28d91187abfd696ea03d0ee86a59864`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_x86_64.whl
Size	1.7 MB
Tags	CPython 3.13 macOS 11.0+ x86-64
SHA-256 checksum How to use checksums	`274287bcd0a74fb03361ef0e509df11209a3eaf64727142e3758a8aafcff8ddf`
BLAKE2b-256 checksum How to use checksums	`bc65d5f53b5613ef015547c8ddbcc88d932765541a681420d8ee611bcdbec776`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_arm64.whl

Download URL	fp_tools_bio-0.2.1-cp313-cp313-macosx_11_0_arm64.whl
Size	1.7 MB
Tags	CPython 3.13 macOS 11.0+ ARM64
SHA-256 checksum How to use checksums	`4509ca1b472de025b1237aa2c6df7d2d47dabb1ed49bc94f2defb46c26a6aeb9`
BLAKE2b-256 checksum How to use checksums	`94c72225fec1a1266724a932eeaad8efc56bc73cfa178df3a2b585bbcdf8a7ef`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp312-cp312-win_amd64.whl

Download URL	fp_tools_bio-0.2.1-cp312-cp312-win_amd64.whl
Size	1.7 MB
Tags	CPython 3.12 Windows x86-64
SHA-256 checksum How to use checksums	`5af0839b3c5dc7f4ec6f4d1ba3cb7b1999d2ba91532915316319c56d7792b6a8`
BLAKE2b-256 checksum How to use checksums	`3be6c3619022e28c97ba66fd8c00ab455a2cfd41ab6b3b3427f464ef2ce55055`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
Size	3.0 MB
Tags	CPython 3.12 Linux glibc 2.17+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`f28aa7875f7cda2e35df27176c02b2d631b1f25e1fc038f27c71242eef1f3681`
BLAKE2b-256 checksum How to use checksums	`4b1aa4ca55df88fdcae0f0c2ee25f1b991f47fa52fe5d33cdf2f24ecd6c60ed6`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl

Download URL	fp_tools_bio-0.2.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
Size	3.0 MB
Tags	CPython 3.12 Linux glibc 2.17+ ARM64 Linux glibc 2.28+ ARM64
SHA-256 checksum How to use checksums	`5ad855dfe5fbf2305f9973e27f8fee3f28456d9fe53d0c68b829178272b0d907`
BLAKE2b-256 checksum How to use checksums	`0f91d60da1e593b2b9fea821680878d028d36f39fff66aa8591782fa9c06a06c`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_x86_64.whl
Size	1.7 MB
Tags	CPython 3.12 macOS 11.0+ x86-64
SHA-256 checksum How to use checksums	`adbc8f52ac56e6862fa8daf15709ccab3b714ac3ecec99ad24980d89a14a0c67`
BLAKE2b-256 checksum How to use checksums	`aada38136e6e8a7c52a711873ec0dab7c1eecdd4f52bc72a6d5c8701d3e2af99`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_arm64.whl

Download URL	fp_tools_bio-0.2.1-cp312-cp312-macosx_11_0_arm64.whl
Size	1.7 MB
Tags	CPython 3.12 macOS 11.0+ ARM64
SHA-256 checksum How to use checksums	`0bc877856e481389c13b06f8edbc867a9aa94e9f4c446f3647e724a186454931`
BLAKE2b-256 checksum How to use checksums	`516ac2fd51586ea9f705b94f47f7e3dbdf9d9a63d7fced18f109c9f23a73bfd5`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp311-cp311-win_amd64.whl

Download URL	fp_tools_bio-0.2.1-cp311-cp311-win_amd64.whl
Size	1.7 MB
Tags	CPython 3.11 Windows x86-64
SHA-256 checksum How to use checksums	`6a119e5d8aa6bbbf7539ed464f14ac43e9902ba49c73a1d34d47e4de107b4e84`
BLAKE2b-256 checksum How to use checksums	`d4482f1be985663e5f72f8bd3e32bdf03668cf53ac19f193ee21e32c78bfa594`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
Size	3.0 MB
Tags	CPython 3.11 Linux glibc 2.17+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`bf7b4a2d4bda5d836c46c249655d6360677b550adfbeb8af55d4980b0fd8ef5f`
BLAKE2b-256 checksum How to use checksums	`65e193a9bd2a60016be0add447613f880a62761cfe2f751c7a7244a6551fd502`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl

Download URL	fp_tools_bio-0.2.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
Size	3.0 MB
Tags	CPython 3.11 Linux glibc 2.17+ ARM64 Linux glibc 2.28+ ARM64
SHA-256 checksum How to use checksums	`007f45f069f5530e74fca96a793e917affe3f8cea6d25509d4c5bfc7f1eea67e`
BLAKE2b-256 checksum How to use checksums	`cbba07922d7baf025b43f2d48bc8af75b6d6d0ac7d150cb3f2e88a3435bf8322`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_x86_64.whl

Download URL	fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_x86_64.whl
Size	1.7 MB
Tags	CPython 3.11 macOS 11.0+ x86-64
SHA-256 checksum How to use checksums	`3b45da48b1e53b33a2cd69e8222b0e224418c16f143bb77dd904529136401de9`
BLAKE2b-256 checksum How to use checksums	`8785c75ec7b9e97e664b930d04f401c312ef3e734c5676be51d9b653ff9c7211`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`

Release files / fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_arm64.whl

Download URL	fp_tools_bio-0.2.1-cp311-cp311-macosx_11_0_arm64.whl
Size	1.7 MB
Tags	CPython 3.11 macOS 11.0+ ARM64
SHA-256 checksum How to use checksums	`0e1f937fbe94bb145d0f5178ef7c5c90fadc52fdc0067f9b284e1b4c0018715d`
BLAKE2b-256 checksum How to use checksums	`2f71f4e2a0d777560c3fc3b3ed635d6c669ee8c8f727dce9793c52bd1f6a4d72`
Upload date	Aug 26, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.12.14`