bio-proteomics-dia-analysis
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Covers library-free and library-based workflows for deep proteome profiling.
npx skills add majiayu000/claude-skill-registry --skill dia-analysis-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# DIA Proteomics Analysis ## DIA-NN Library-Free Analysis ```bash # Library-free mode (generates library from data) diann \ --f sample1.mzML \ --f sample2.mzML \ --lib "" \ --threads 8 \ --verbose 1 \ --out report.tsv \ --qvalue 0.01 \ --matrices \ --out-lib generated_lib.tsv \ --gen-spec-lib \ --predictor \ --fasta uniprot_human.fasta \ --fasta-search \ --min-fr-mz 200 \ --max-fr-mz 1800 \ --met-excision \ --cut K*,R* \ --missed-cleavages 1 \ --min-pep-len 7 \ --max-pep-len 30 \ --min-pr-mz 300 \ --max-pr-mz 1800 \ --min-pr-charge 1 \ --max-pr-charge 4 \ --unimod4 \ --var-mods 1 \ --var-mod UniMod:35,15.994915,M \ --reanalyse \ --smart-profiling ``` ## DIA-NN with Spectral Library ```bash # Use pre-built or predicted library diann \ --f sample1.mzML \ --f sample2.mzML \ --lib spectral_library.tsv \ --threads 8 \ --verbose 1 \ --out report.tsv \ --qvalue 0.01 \ --matrices \ --reanalyse \ --smart-profiling ``` ## DIA-NN Output Files ``` report.tsv # Main quantification report (long format) report.stats.tsv # Run statistics report.pg_matrix.tsv # Protein group quantities (wide format) report.pr.matrix.tsv # Precursor quantities (wide format) report.gg_matrix.tsv # Gene group quantiti
- DIA-NN Library-Free Analysis
- DIA-NN with Spectral Library
- DIA-NN Output Files
- Load DIA-NN Results in R
- Load DIA-NN Results in Python
- MSFragger-DIA Analysis
- Spectronaut Export Processing
- DIA Quality Metrics
- Match Between Runs
- DIA vs DDA Comparison
- Related Skills
Library-free mode (generates library from data) diann \ Use pre-built or predicted library MSFragger for DIA (alternative to DIA-NN) Requires FragPipe GUI or command-line workflow Generate predicted library with EasyPQP easypqp library \ Convert to DIA-NN format easypqp convert \ DIA-NN MBR is automatic with --reanalyse flag
What does the bio-proteomics-dia-analysis skill do?
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Covers library-free and library-based workflows for deep proteome profiling.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill dia-analysis-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.