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loqculate

This wiki documents loqculate v0.4.1. Run loqculate --version before following version-specific behavior.

loqculate reads a calibration export, joins run filenames to concentrations, fits one model per peptide, and writes LOD, LOQ, and optional plots. The default model is PiecewiseCF. Default LOQ is bootstrap.

Start

1. Install from source (not on PyPI).
2. Run the demo fit.
3. Open the CLI reference when a flag does not do what you expected. Several flags are parsed for every model and only forwarded to some of them.

Models

Each model has its own page. Models is only the comparison.

• PiecewiseCF: default. Closed-form knot search. Bootstrap LOQ, optional delta.
• PiecewiseWLS: same piecewise mean function, scipy TRF solver.
• EmpiricalCV: replicate CVs at calibration levels. No LOD.
• OriginalWLS: Pino 2020 WLS path (old/calculate-loq.py).
• OriginalCV: Pino 2020 CV path (old/loq_by_cv.py).

Elsewhere

• Python API
• Input formats
• Benchmarks
• Troubleshooting
• Development