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lehtiolab/nf-deqms : Output

This document describes the output produced by the pipeline.

Output files

The output is a number of text, SQLite and HTML files. Depending somewhat on inputs, the following can be obtained from the output directory:

  • a peptide table (TSV)
  • protein and genes tables (TSV)
  • a QC report (HTML)

File columns

For all output tables, the columns are identical as input tables, and the following fields get added or substituted:

DEqMS

DEqMS is an R package for testing differential protein expression in quantitative proteomic analysis, built on top of the Limma package. PMID 32205417