signatomics

Python tools for Olink proteomics data: read, quality control, bridging and sample metadata, with every step reported.

signatomics is a family of Python tools for finding biomarker signatures in omics data. The first module, signatomics.olink, works with Olink (PEA) proteomics data. More modules will build on it later.

📖 Documentation: https://signatomics.elenastamatelou.com

Status: in development (version 0.0.1). The Olink module reads data, controls its quality, bridges plates and adds your sample metadata; signatomics.stats compares groups and correlates. Functions may still change before the first release.

What it does today

import signatomics.olink as so

data  = so.read_npx(so.example_file())    # a synthetic example NPX file; your own: so.read_npx("my_npx_file.csv")
so.qc_report(data)                        # look at quality: your data stays as it is
clean = so.prepare(so.example_file())     # read, quality control, bridging and sample metadata in one call

Each step also exists on its own, with every choice visible: read_npx, qc_report → apply_qc, bridge_check → bridge_plates, add_sample_info.

• Reading: NPX files in long format and older wide (NPX Manager) files; .csv, .txt, .xlsx and .parquet; European decimal commas, "No Data" cells, TRUE/FALSE written in other languages.
• Quality control: a quality check and charts that leave your data as it is, then your choices applied, with every removal listed.
• Bridging: per-protein plate correction, with the detection limits shifted along, and an independent PCA check.
• Sample metadata: adds your sample metadata (demographics, clinical data, ...) and reports every ID without a match.
• Statistics: the analysis table (to_wide: one row per sample), then compare_groups and correlate on every assay, with effect sizes, 95% intervals and an FDR; plot_volcano.
• Charts: interactive Plotly charts in one style, colour-blind safe; sample IDs hidden by default.

Install

pip install "signatomics[olink] @ git+https://github.com/ElenaStamatelou/signatomics"

Requires Python 3.10 or newer. See Start in 5 minutes.

The family

Module	Data	Status
signatomics.olink	Olink (PEA) proteomics: Target 96/48, Explore, Explore HT, Reveal	in development
signatomics.stats	compare groups, correlate: every assay, effect sizes, FDR	in development
core	one standard table, combining data types, biomarker signature with nested cross-validation	planned
more modules	e.g. ELISA, microbiome	ideas

Repository layout

Folder	What
src/signatomics/	the package
tests/	automatic tests (pytest)
analyses/	worked analyses of public data (Jupyter notebooks)
website/	the documentation website (MkDocs Material)
docs/	function reference pointer, notes on the example datasets

Public datasets stay outside this repository; the only data inside are the small, synthetic example files of the package. See docs/datasets.md.

Author

Elena Stamatelou

signatomics is an independent project. It is not affiliated with or endorsed by Olink or Thermo Fisher Scientific. Olink is a trademark of Thermo Fisher Scientific.