Skip to content
@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

Showing 10 of 17 repositories
  • paftacular Public

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

    tacular-omics/paftacular's past year of commit activity
    Python 1 MIT 5 2 (2 issues need help) 2 Updated Nov 11, 2026
  • unimodpy Public

    Python library, API, and MCP server for the UNIMOD mass spectrometry modifications database

    tacular-omics/unimodpy's past year of commit activity
    Python 1 MIT 4 0 1 Updated Nov 11, 2026
  • 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.

    tacular-omics/pefftacular's past year of commit activity
    Python 1 MIT 1 2 (1 issue needs help) 1 Updated Nov 11, 2026
  • tacular Public

    Python lookups for amino acids, elements, and proteomics PTM ontologies (UNIMOD, PSI-MOD, RESID, XLMOD, GNOme)

    tacular-omics/tacular's past year of commit activity
    Python 1 MIT 3 0 1 Updated Nov 11, 2026
  • mzmlpy Public

    Fast, lazy mzML reader for Python: typed models, gzip random access, validation, Numpress/zstd decoding

    tacular-omics/mzmlpy's past year of commit activity
    Python 4 MIT 0 2 1 Updated Nov 11, 2026
  • fastatacular Public

    Pure-Python library for reading and writing FASTA sequence files with UniProt-style header parsing.

    tacular-omics/fastatacular's past year of commit activity
    Python 0 MIT 1 1 (1 issue needs help) 1 Updated Nov 11, 2026
  • uniprotptmpy Public

    Python library, API, and MCP server for the UniProt PTM controlled vocabulary

    tacular-omics/uniprotptmpy's past year of commit activity
    Python 1 MIT 2 2 (2 issues need help) 0 Updated Nov 11, 2026
  • psimodpy Public

    Python library, API, and MCP server for the PSI-MOD protein modification ontology

    tacular-omics/psimodpy's past year of commit activity
    Python 1 MIT 0 3 0 Updated Nov 11, 2026
  • tdfpy Public

    Python reader for Bruker timsTOF (.d) data: DDA/DIA/PRM, fast centroiding and noise filtering

    tacular-omics/tdfpy's past year of commit activity
    Python 8 MIT 1 4 0 Updated Nov 10, 2026
  • peptacular Public

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

    tacular-omics/peptacular's past year of commit activity
    Python 21 MIT 7 9 (1 issue needs help) 1 Updated Nov 10, 2026
View all repositories

People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages

Python