Documentation · Output demo with ENCODE cancer cell lines · GUI demo · PyPI
fp-tools is a command-first toolkit for ATAC-seq bias correction, footprint
scoring, motif analysis, replicate-aware comparisons, and single-cell
footprint signatures. The optional GUI and YAML runner call the same commands.
Install
pip install fp-tools-bio
For the GUI:
pip install "fp-tools-bio[gui]"
fp-tools-gui
Bulk ATAC-seq
bulk-footprinting runs the complete analysis from aligned BAM and peak files.
FASTQ preparation remains available separately through prepare-atac.
bulk-footprinting \
--sample-table samples.tsv \
--comparison-table comparisons.tsv \
--genome hg38.fa.gz \
--blacklist hg38.blacklist.bed \
--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.
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 |
| 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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