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

External genomics programs are downloaded into a private, versioned cache on first use. They do not need to be installed separately. Docker remains an optional reproducible backend.

Bulk ATAC-seq

bulk-footprinting can run from FASTQ files or public run accessions through the final interactive comparison report.

bulk-footprinting \
  --reads-table reads.tsv \
  --comparison-table comparisons.tsv \
  --genome hg38 \
  --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.

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	`prepare-atac`, `atac-correct`, `call-footprints`, `match-motifs`, `diff-footprints`, `normalize-bigwig`
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.

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

fp_tools_bio-0.2.0rc6.tar.gz (1.5 MB view details)

Uploaded Aug 20, 2026 Source

Built Distributions

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

fp_tools_bio-0.2.0rc6-cp313-cp313-win_amd64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.13Windows x86-64

fp_tools_bio-0.2.0rc6-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.0 MB view details)

Uploaded Aug 20, 2026 CPython 3.13manylinux: glibc 2.17+ x86-64manylinux: glibc 2.28+ x86-64

fp_tools_bio-0.2.0rc6-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (2.9 MB view details)

Uploaded Aug 20, 2026 CPython 3.13manylinux: glibc 2.17+ ARM64manylinux: glibc 2.28+ ARM64

fp_tools_bio-0.2.0rc6-cp313-cp313-macosx_11_0_x86_64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.13macOS 11.0+ x86-64

fp_tools_bio-0.2.0rc6-cp313-cp313-macosx_11_0_arm64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.13macOS 11.0+ ARM64

fp_tools_bio-0.2.0rc6-cp312-cp312-win_amd64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.12Windows x86-64

fp_tools_bio-0.2.0rc6-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.0 MB view details)

Uploaded Aug 20, 2026 CPython 3.12manylinux: glibc 2.17+ x86-64manylinux: glibc 2.28+ x86-64

fp_tools_bio-0.2.0rc6-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (3.0 MB view details)

Uploaded Aug 20, 2026 CPython 3.12manylinux: glibc 2.17+ ARM64manylinux: glibc 2.28+ ARM64

fp_tools_bio-0.2.0rc6-cp312-cp312-macosx_11_0_x86_64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.12macOS 11.0+ x86-64

fp_tools_bio-0.2.0rc6-cp312-cp312-macosx_11_0_arm64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.12macOS 11.0+ ARM64

fp_tools_bio-0.2.0rc6-cp311-cp311-win_amd64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.11Windows x86-64

fp_tools_bio-0.2.0rc6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (3.0 MB view details)

Uploaded Aug 20, 2026 CPython 3.11manylinux: glibc 2.17+ x86-64manylinux: glibc 2.28+ x86-64

fp_tools_bio-0.2.0rc6-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (3.0 MB view details)

Uploaded Aug 20, 2026 CPython 3.11manylinux: glibc 2.17+ ARM64manylinux: glibc 2.28+ ARM64

fp_tools_bio-0.2.0rc6-cp311-cp311-macosx_11_0_x86_64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.11macOS 11.0+ x86-64

fp_tools_bio-0.2.0rc6-cp311-cp311-macosx_11_0_arm64.whl (1.7 MB view details)

Uploaded Aug 20, 2026 CPython 3.11macOS 11.0+ ARM64

File details

Details for the file fp_tools_bio-0.2.0rc6.tar.gz.

File metadata

Download URL: fp_tools_bio-0.2.0rc6.tar.gz
Upload date: Aug 20, 2026
Size: 1.5 MB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: twine/7.0.0 CPython/3.12.14

File hashes

Hashes for fp_tools_bio-0.2.0rc6.tar.gz
Algorithm	Hash digest
SHA256	`7ed6e86555d3b20ab3d89270ed4d9d4a09565570e6becbf5d594dc70890591b5`
MD5	`e49aca6f81d867ac09f2de8091e6535d`
BLAKE2b-256	`2f58429fda34e7950aa02c110f69308e8ffd0b7a2b4ee0647f6239f60df57de4`

Algorithm	Hash digest
SHA256	`26e5f476e9fca4dd290219c7c89f06996679b0ff66121dcc314566ad9412f863`
MD5	`3fe0db84ce137e25d406c03463e6c8fb`
BLAKE2b-256	`532bb4af944a99c2dc2fafa26fe53b6087957a00934231ad5a4b44bc29e99922`

Algorithm	Hash digest
SHA256	`624d2de9c5afb2142114e7b6e6748f7bccec0a8f963f77c282b8c3278d544001`
MD5	`0ce6214aaa97c0e58cc5616cadfe26fe`
BLAKE2b-256	`44f67797f1daeec658eb5626b947f6795950347fb3c8501b874df47d68719dcf`

Algorithm	Hash digest
SHA256	`81b7b565523c9a62fa815a4c353726285801a5738c2cfbb5471f69c32587277e`
MD5	`ce823087c6f3505bdbdc8500b178594a`
BLAKE2b-256	`94e04c44eff090de26e72bb93dbc2bf27ac89dc62745d60232f4b16486f736b0`

Algorithm	Hash digest
SHA256	`7877a2b719e2d15ab9c58f586b1890d82922e40d057e508fd5a72559f358908b`
MD5	`b2b8a409d65aea2931694b053a067f7b`
BLAKE2b-256	`f1b98443e897ef6d4d8c4c6ad4479830f1c3f5732741a99eeacfa6456b9a834c`

Algorithm	Hash digest
SHA256	`3a55c409dbcbf8cb43db62b420cd86febf8ebef03d655e611f90af2d9c6f4caa`
MD5	`0a51ee31e629723426008cd1183c2869`
BLAKE2b-256	`0c703a1f7f3885d592b629c569a2b9837ff75c5ee881825cc4e797ef09cd5ebd`

Algorithm	Hash digest
SHA256	`aba20acc48ae38be826c25f9de291de22d4b755d90656e79a1e3a23c3291f531`
MD5	`a3a362f8a1120c6eecb55fc5061f9f0e`
BLAKE2b-256	`0c3f9ef8ad611307426a12b8b608806619a9e6d6b79611ed8b3f536705458b74`

Algorithm	Hash digest
SHA256	`83c5e8fbb270df8da217556cd8c6a975ad61b2b64ead938405be044cac91474c`
MD5	`dce02ad2c7fa89108dbcffe67fc0dcb6`
BLAKE2b-256	`ad7b6c231473f074cf1392abba897216febc2e16f00ff721a12531b0eaba53d9`

Algorithm	Hash digest
SHA256	`71665d57fe3d8aebe5f9cd4dc6cfc8ce54d7d8758a3a6098a0a2318cef014624`
MD5	`11c0e66a484200eaeba7bc52a114d363`
BLAKE2b-256	`3e4f3e47c314b7a4c92c6ce9f6c2d4884b58d90abace05fbd891d22078c01152`

Algorithm	Hash digest
SHA256	`3ee27453eeecb2f79a8512bf4791a5dc70721a7ff223487b967894df667ddf30`
MD5	`8fb3621b860f3781b5693fb6c5d9d587`
BLAKE2b-256	`702cded664ddead954ee0c3c75c8b28312efb316f183ca37a95a15b2d99023de`

Algorithm	Hash digest
SHA256	`d88661123f7bc583dcfd9ab11cdfd9eab60b687e6c93e8f46c5dc0e92c6e5d5a`
MD5	`72e535ddf1569e716f12969797352eaa`
BLAKE2b-256	`c4a2d88a5cfc3d965743ca1f13be440b06cc0c3af1dff32cf0fedc34dc444621`

Algorithm	Hash digest
SHA256	`5bcf5c976659e66c68f3b48aca05fe886b9ef85323484b6b413e76fe6b33f968`
MD5	`29fed6763bb6be17e28b80bb3e067143`
BLAKE2b-256	`4638b23d019f56d35f1acd7ef79786acad919c89529c0e2141d237db6ee59e51`

Algorithm	Hash digest
SHA256	`da4890a4eab759ad5c459ef84de9f997f15c8b918c76d523e50567ff1fcdeb61`
MD5	`44daffb864a66cc6c7ff959dc60d0d22`
BLAKE2b-256	`6a3f5cfaa5aacaf6f5873a4115f059324a044de8fb1a2432bf8dbe7f6aa93479`

Algorithm	Hash digest
SHA256	`4d741b1d5ba920e8befe95f580c94f40fcfca3bcc8ce6731ff972ee8db0cab6a`
MD5	`0bf356eeb0f89b1521f7f9cd61ce26b0`
BLAKE2b-256	`71a3ef4967429daf5472e89649fcc0d340028f7804f378b3868b94a5f6ba06aa`

Algorithm	Hash digest
SHA256	`b97cf44ac1e279b621a8b248f82cef6ec3a89be676a07556d73c917b9b1cf2ff`
MD5	`96463283d0ad74799bdb1c165980a9e0`
BLAKE2b-256	`4b5075de4b802bcead76a0c3eaa98e25503714afee33e80d33ce84563e25332d`

Algorithm	Hash digest
SHA256	`46eb56711ca67cce96fb9f03883a26fcd4f9f60589fb7b7d06d32f2251b645d4`
MD5	`4be9c4a60914ae754a1b44d7f4d785af`
BLAKE2b-256	`a4beb2db5e611224d6f1b51deaec030ace1db3c40013d40168054ef1d5eccac2`

fp-tools-bio 0.2.0rc6

Install

Bulk ATAC-seq

Single-cell ATAC-seq

Main commands

Project links

Key dates

1 maintainer

Credits

License expression

Requires

Provides Extra

Tags

Classifiers

Download files

Source Distribution

Built Distributions

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

File details

File metadata

File hashes

Release history Release notifications | RSS feed