Getting Started

Getting started

After Installation, from the repository root:

uv run loqculate fit data/demo/one_protein.csv data/demo/filename2samplegroup_map.csv

The demo export is EncyclopeDIA-style (numFragments in the header). The command writes figuresofmerit.csv in the current directory. --plot y is the default, so calibration figures go there too.

Concentration map

Second positional argument. Two columns: filename (basename, no directory) and concentration (numeric).

filename,concentration
sample_1ng_rep1.raw,1.0
sample_1ng_rep2.raw,1.0
sample_5ng_rep1.raw,5.0

How each reader joins on that file is on Input formats. Generic CSV still requires the path even though it does not join.

Output

fit writes peptide, LOD, LOQ, slope, intercept_linear, intercept_noise. Infinite LOD or LOQ is a stored result, not a crash. CV-only models leave the slope and intercept cells empty.

compare writes overlay plots only. It does not write figuresofmerit.csv.

uv run loqculate compare data/demo/one_protein.csv data/demo/filename2samplegroup_map.csv --plot y

Default --models is piecewise_cf,piecewise_wls.

Next

Flags: CLI reference. Models: Models. Python: Python API.