limpa-run-dea
Run limpa differential expression analysis on protein-level data.
Skill by Alexander-Sol
Chalk Labs
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Install
Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.
npx agentmarket install skill/alexander-sol-limpa-run-dea
Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.
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About
Use cases: design, data
Reviews
Write a reviewNo reviews yet. Installed it? Reviews come from verified installers only. How reviews work
Permissions
What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.
- Tools
- No tools found
- Secrets
- None asked for
- Install scripts
- None found
Network hosts it talks to 1
codeload.github.com· found in install command
Files it touches
~/.claude/skills/limpa-run-dea
What's inside
- Skill name
limpa-run-dea- Description
- Run limpa differential expression analysis on protein-level data. Requires dat.protein, design, and contrast.matrix in the R session.
- License
- unknown
- Instructions
- 21 lines in SKILL.md · view on GitHub
Files (1)
- SKILL.md
The license isn't open source, so the instructions aren't shown here. Read SKILL.md on GitHub
More from Alexander-Sol/ProteomicsKit
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opencode-load-peptide
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Load a FlashLFQ/MetaMorpheus AllQuantifiedPeptides.tsv into a limpa-compatible EList.
SkillDFreshness: DClaude Code +9 - 0.402score
limpa-fit-dpc
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Fit the Detection Probability Curve (DPC) for the limpa protein DEA workflow.
SkillDFreshness: DClaude Code +9 - 0.402score
build-design
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Interactively build the metadata, design matrix, and contrast matrix for a DEA workflow.
SkillDFreshness: DClaude Code +9 - 0.402score
ptm-plot-mod-summary
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Draw a stacked bar chart comparing modification category composition between all peptides and DA peptides.
SkillDFreshness: DClaude Code +9 - 0.402score
ptm-run-dea
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Run differential expression analysis on peptidoform fraction data (dpcDE -> eBayes).
SkillDFreshness: DClaude Code +9 - 0.402score
limma-run-dea
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Run limma differential expression analysis on protein-level data (lmFit -> contrasts.fit -> eBayes).
SkillDFreshness: DClaude Code +9 - 0.402score
limpa-plot-volcano
Alexander-Sol
Draw a volcano plot from DEA results (logFC vs -log10 adj.P.Val).
SkillDFreshness: DClaude Code +9 - 0.402score
limpa-summarize-proteins
Alexander-Sol
Summarize peptide-level data to protein level using DPC-weighted quantification (limpa dpcQuant).
SkillDFreshness: DClaude Code +9 - 0.402score
opencode-plot-missing
Alexander-Sol
Plot per-run missing-value proportions for the active R session.
SkillDFreshness: DClaude Code +9 - 0.402score
ptm-normalize-to-protein
Alexander-Sol
Compute peptidoform fractions by subtracting parent protein abundance from peptide intensity.
SkillDFreshness: DClaude Code +9 - 0.399score
opencode-plot-mds
Alexander-Sol
Plot a multi-dimensional scaling (MDS) plot at the peptide level for the active R session.
SkillDFreshness: DClaude Code +9 - 0.399score
opencode-plot-dpc
Alexander-Sol
Fit and plot the Detection Probability Curve (DPC) for the active R session.
SkillDFreshness: DClaude Code +9
Signals
- Stars
- 0
- Forks
- 0
- Open issues
- 0
- Last commit (this folder)
- Apr 10, 2026 (6 months ago)
From GitHub (fetched Oct 24, 2026).
Details
- License
- License unknown
- Repository
- github.com/Alexander-Sol/ProteomicsKit
- First seen
- Oct 24, 2026
- Last checked
- Oct 24, 2026
- Source
- GitHubgithub-graphql
More from Alexander-Sol
- 0.405score
opencode-load-peptide
Alexander-Sol
Load a FlashLFQ/MetaMorpheus AllQuantifiedPeptides.tsv into a limpa-compatible EList.
SkillDFreshness: DClaude Code +9 - 0.402score
build-design
Alexander-Sol
Interactively build the metadata, design matrix, and contrast matrix for a DEA workflow.
SkillDFreshness: DClaude Code +9 - 0.402score
limpa-fit-dpc
Alexander-Sol
Fit the Detection Probability Curve (DPC) for the limpa protein DEA workflow.
SkillDFreshness: DClaude Code +9 - 0.402score
ptm-plot-mod-summary
Alexander-Sol
Draw a stacked bar chart comparing modification category composition between all peptides and DA peptides.
SkillDFreshness: DClaude Code +9 - 0.402score
ptm-run-dea
Alexander-Sol
Run differential expression analysis on peptidoform fraction data (dpcDE -> eBayes).
SkillDFreshness: DClaude Code +9 - 0.402score
limma-run-dea
Alexander-Sol
Run limma differential expression analysis on protein-level data (lmFit -> contrasts.fit -> eBayes).
SkillDFreshness: DClaude Code +9
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Cite this page
limpa-run-dea skill. Agent Mart. https://agentmart.dev/skills/alexander-sol-limpa-run-dea (last updated 2026-10-24)