fastsig

Fast publication-quality signal heatmaps and boxplots, with a Rust-accelerated implementation of the most commonly used signal-processing primitives.

pip install fastsig

fastsig --help
fastsig pipeline   --help     # end-to-end BAM/bigWig → heatmap+boxplot
fastsig function   --help     # gene-set heatmap from GMT
fastsig gene       --help     # gene-body heatmap from GTF
fastsig gtf-to-bed --help     # extract genes/transcripts from GTF.gz

Subcommands

pipeline          End-to-end BAM/bigWig → matrix → heatmap + boxplot driver
function          Gene-set heatmap + boxplot from one or more GMT/text files
gene              Gene-body heatmap + boxplot from a GTF or gene BED
plot-heatmap-box  Compute a signal matrix then render heatmap + boxplot
bam-coverage      Convert BAM to normalized bigWig/bedGraph coverage
bigwig-compare    Combine two bigWigs (log2/ratio/subtract/add/mean) into one
compute-matrix    Build per-region signal matrices from bigWigs (.mat.gz)
gtf-to-bed        Extract genes or transcripts from GTF(.gz) to BED6

Documentation

Full user guide (Chinese) — installation, every subcommand's parameter table, end-to-end recipes, input format reference, FAQ, and how to build from source:

📖 https://github.com/typekey/deeptools_rust/blob/main/docs/fastsig_usage.md

See the project README for benchmarks, architecture notes, and demo figures.

License

MIT

Project links

Data verified by PyPI on Aug 29, 2026
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Credits

Author: fastsig authors

GitHub Statistics

Data verified by PyPI on Aug 29, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
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Requires

Python >=3.9

Provides Extra

deeptools

Tags

bioinformatics chip-seq atac-seq deeptools heatmap bigwig

Classifiers

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