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 \
--outdir project \
--cores 8
The hg38 and mm10 labels use checksum-verified FASTA and blacklist files
from the managed reference cache. A custom FASTA path and optional custom
blacklist can be supplied instead. 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.
1 maintainer
Metadata
1 maintainer
Release files for fp-tools-bio 0.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| fp_tools_bio-0.2.2.tar.gz | 1.5 MB | Details |
Built distributions (wheels)
Total release size: 34.9 MB
Release files / fp_tools_bio-0.2.2.tar.gz
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| Tags | Source |
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Release files / fp_tools_bio-0.2.2-cp313-cp313-win_amd64.whl
| Download URL | fp_tools_bio-0.2.2-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 1.7 MB |
| Tags | CPython 3.13 Windows x86-64 |
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Release files / fp_tools_bio-0.2.2-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
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Release files / fp_tools_bio-0.2.2-cp313-cp313-macosx_11_0_x86_64.whl
| Download URL | fp_tools_bio-0.2.2-cp313-cp313-macosx_11_0_x86_64.whl |
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