fp-tools analyzes ATAC-seq and CUT&Tag data to measure chromatin footprints
and compare motif-associated signals. Start with aligned reads and peak files
for bulk analysis, or fragments and cell annotations for single-cell analysis.
Run each step from the command line, save workflows as YAML, or use the GUI.
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 --upgrade fp-tools-bio
bulk-footprinting --help
To open the browser interface, run fp-tools-gui. See the
installation guide
for desktop setup and remote-server instructions. Optional de novo motif tools
are downloaded automatically on first use.
Bulk ATAC-seq
bulk-footprinting runs from coordinate-sorted BAM/BAI files and matching peak
BED files through the final interactive comparison report.
Prepare samples.tsv with one row per biological sample and the columns
sample, condition, bam, and peaks. In comparisons.tsv, use comparison,
cond1, and cond2 to name each comparison and its two conditions. The
bulk workflow guide
provides minimal tables and explains the required inputs.
bulk-footprinting \
--sample-table samples.tsv \
--comparison-table comparisons.tsv \
--genome hg38 \
--outdir project
The workflow uses all available cores by default. Stage progress and command messages appear live in your terminal and are also saved in the project logs.
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.
The single-cell workflow guide explains the annotation columns and AnnData file required for this command.
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 0.2.7
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-0.2.7.tar.gz | 1.5 MB | Details |
Built distributions (wheels)
Total release size: 35.1 MB
Release files / fp_tools_bio-0.2.7.tar.gz
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Release files / fp_tools_bio-0.2.7-cp313-cp313-win_amd64.whl
| Download URL | fp_tools_bio-0.2.7-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-0.2.7-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-0.2.7-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
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Release files / fp_tools_bio-0.2.7-cp313-cp313-macosx_11_0_x86_64.whl
| Download URL | fp_tools_bio-0.2.7-cp313-cp313-macosx_11_0_x86_64.whl |
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