bio-proteomics-dia-analysis
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-proteomics-dia-analysis --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.
## Version Compatibility Reference examples tested with: numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # DIA Proteomics Analysis **"Analyze my DIA proteomics data"** → Process data-independent acquisition MS data to identify and quantify proteins using library-free or library-based workflows. - CLI: `diann` for end-to-end DIA analysis with neural network scoring - CLI: `EncyclopeDIA` for chromatogram library-based quantification ## DIA-NN Library-Free Analysis **Goal:** Run DIA proteomics analysis without a pre-built spectral library, generating one from the data itself. **Approach:** Use DIA-NN in library-free mode with FASTA-based in silico digestion and deep learning prediction. ```bash # Library-free mode (generates library from data) diann \ --f sa
- Version Compatibility
- 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. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-proteomics-dia-analysis --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.