prolfqua

Run, set up, or troubleshoot the prolfquapp differential expression analysis CLI, especially prolfqua_dea.sh, prolfqua_dataset.sh, prolfqua_yaml.sh, prolfqua_contrasts.sh, prolfqua_qc.sh, dataset annotation design, CONTROL/ContrastName/Contrast columns, paired designs with subject/bioreplicate blocking, two-factor/factorial contrasts, and the prolfquapp R functions that copy or drive those scripts. Use when users ask how to get prolfqua_dea.sh into a working directory, prepare the annotation/YAML inputs, define contrasts, choose the software key, run DEA for DIA-NN, MaxQuant, FragPipe, Spectronaut/BGS, MSstats, MZMine, or debug missing scripts/config/report outputs.