bio-workflows-proteomics-pipeline
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.
npx skills add BioTender-max/awesome-bio-agent-skills --skill proteomics-pipeline --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: MSnbase 2.28+, ggplot2 3.5+, limma 3.58+, DEqMS 1.20+, ashr 2.2+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Proteomics Pipeline **"Process my proteomics data from raw MS files to differential abundance"** → Orchestrate data import (pyopenms/MaxQuant), QC assessment, protein quantification, normalization, differential abundance testing (limma/DEqMS, or MSstats for feature-level designs), and PTM analysis. ## Pipeline Overview ``` Raw MS Data (mzML) ──> MaxQuant/DIA-NN ──> proteinGroups.txt │ ▼ ┌────────────────────────────────────────────┐ │ proteomics-pipeline │ ├────────────────────────────────────────────┤ │ 1. Data Import & Filtering │ │ 2. Log2 Transform & Normalization │ │ 3. Missing Value Imputation │ │ 4. QC: PCA, Correlation │ │ 5. Differential Abundance (limma/MSstats) │ │ 6. Visualization & Export │ └────────────────────────────────────────────┘ │
- Version Compatibility
- Pipeline Overview
- Complete R Workflow
- MSstats Workflow
- QC Checkpoints
- Workflow Variants
- TMT/iTRAQ Isobaric Labeling
- SILAC Workflow
- DIA-NN Workflow
- Related Skills
What does the bio-workflows-proteomics-pipeline skill do?
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill proteomics-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.