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@tacular-omics

tacular-omics

Various omics-based software tools
README.md

tacular-omics

Open-source Python tools for proteomics and mass spectrometry, built in the Yates Lab at Scripps Research. The packages cover the pipeline end to end: sequence and modification handling, raw-file and standard-format I/O, and spectrum processing — designed to be composed together or used on their own.

All projects are MIT-licensed and PRs are welcome.

Contributing

New contributors are welcome, and every package is set up the same way, so what you learn on one applies to all of them.

  • Find something to work on: good first issues need no knowledge of the codebase. Help wanted issues are the next step: each one names the files to read first and the test that shows it is done.
  • Claim it first: comment on the issue before you start. One issue, one contributor. When two pull requests arrive for the same issue, the one that was claimed first is reviewed.
  • Ask: every repository has Discussions enabled for usage questions and design ideas.
  • What to expect: every pull request runs the full test matrix on Linux, macOS and Windows, and a maintainer reviews it. Do not change the version or uv.lock.

Packages

Sequences & modifications

Package Description Links
tacular Lookups for amino acids, elements, and proteomics PTM ontologies (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme) PyPI · Docs
peptacular Peptide sequence analysis built around ProForma 2.1 notation — masses, fragments, isotopic patterns PyPI · Docs
paftacular Parsing and serializing mzPAF (Peak Annotation Format) for annotating fragment ions PyPI · Docs
psimodpy Library, API, and MCP server for the PSI-MOD protein modification ontology PyPI
unimodpy Library, API, and MCP server for the UNIMOD mass spectrometry modifications database PyPI
uniprotptmpy Library, API, and MCP server for the UniProt PTM controlled vocabulary PyPI

Files & formats

Package Description Links
mzmlpy Fast, lazy mzML reader: typed models, gzip random access, validation, Numpress/zstd decoding PyPI · Docs
tdfpy Reader for Bruker timsTOF (.d) data: DDA/DIA/PRM, fast centroiding and noise filtering PyPI · Docs
fastatacular Reading and writing FASTA sequence files with UniProt-style header parsing PyPI
pefftacular Reading and writing PEFF (PSI Extended FASTA Format) files, FASTA's proteomics-annotated superset PyPI
spectrl Self-contained, URL-safe mass spectrum interchange for Python and TypeScript PyPI · Docs

Spectra

Package Description Links
spxtacular Chainable Spectrum API for MS processing: denoising, isotope deconvolution, matching, scoring, plotting PyPI · Docs

Tools

Package Description Links
tdfextractor Extract MS/MS spectra from Bruker timsTOF .d folders and convert them to MS2, MGF, or mzML PyPI
peff_uniprot_fetcher Generate annotated PEFF files from UniProt accessions, taxonomy IDs, or search queries PyPI · Try it in the browser

Pinned Loading

  1. peptacular peptacular Public

    Parse ProForma 2.1 peptide sequences and calculate masses, fragments, and isotopic distributions in Python.

    Python 21 7

  2. paftacular paftacular Public

    Parse and serialize HUPO-PSI mzPAF fragment-ion annotations for mass-spectrometry proteomics in Python.

    Python 1 5

  3. spxtacular spxtacular Public

    Chainable Spectrum API for MS processing: denoising, isotope deconvolution, matching, scoring, plotting

    Python 4 6

  4. pefftacular pefftacular Public

    Python library for reading and writing PEFF (PSI Extended FASTA Format) files. PEFF is a superset of FASTA used in proteomics that carries rich per-entry annotations.

    Python 1 1

Repositories

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