MannLabs

MannLabs/proteomics-agent-skills

Plugin Claude Code

Agent Skills for proteomics data analysis from the Mann Labs.

MannLabs/proteomics-agent-skills

Plugin Claude Code

Transform proteomics search-engine output tables into high-confidence biological insights using best practices: data reading, quality control, normalization, imputation, batch-effect correction, differential expression analysis, and biological interpretation.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Analyze proteomics search engine outputs using alphapepttools with AnnData. Use when (1) analyzing proteomics data from DIA-NN, AlphaDIA, Spectronaut, MaxQuant, or other search engines, (2) quality control and preprocessing of protein/peptide abundance matrices, (3) performing differential expression analysis on…

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Apply code quality standards for scientific data analysis. ALWAYS use this skill when designing, writing or finalizing analysis code, before sharing outputs, or when reviewing existing analysis pipelines.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Evaluate and correct batch effects in proteomics data. Use when (1) assessing if batch effect, technical variation, plate effects, or instrument drift in proteomics context is present and batch correction is needed, (2) applying batch correction algorithms, (3) validating batch correction results.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Drawing findings from proteomics analysis. Use when computational data analysis is complete. Use for investigating biological or clinical impact.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Impute missing values in protein-level proteomics data matrices. Use when (1) preparing proteomics data for downstream analyses requiring complete matrices (PCA, batch correction), (2) evaluating whether imputation is needed, (3) selecting appropriate imputation methods, or (4) assessing imputation quality. Does NOT…

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Interpret biological results from omics analyses. Use when (1) performing overrepresentation analysis (ORA) on significant gene/protein lists, (2) running gene set enrichment analysis (GSEA) on ranked features, (3) querying STRING/UniProt for protein function, or (4) annotating clusters with pathway information.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Evaluate the need for and perform normalization of protein-level proteomics intensity data. Use when (1) assessing whether normalization is needed, (2) selecting normalization methods, (3) applying it. Does NOT cover batch correction or imputation.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Perform quality control for protein-level proteomics data. Use when filtering outlier samples or low-evidence features before downstream analysis. Covers PSM artifact removal, sample QC, feature-level filtering. Does NOT cover normalization, batch correction, or imputation.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Perform differential expression analysis on preprocessed proteomics data. Use this when performing finding testing (t-tests, ANOVA) to identify regulated proteins, and multiple testing correction (FDR). Generates standard visualizations like Volcano plots.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Read proteomics search engine outputs (PSM tables, protein matrices) from search engines like DIA-NN, MaxQuant, Spectronaut, AlphaDIA, MSFragger, Sage. Use for ingesting data, mapping columns to standard names, and initial filtering.

MannLabs/proteomics-agent-skills

Skill Claude CodeCodex

Meta-skill for discovering, orchestrating, and sequencing proteomics analysis skills (reading, QC, preprocessing, statistics, interpretation, findings). Use at the start of any proteomics task to identify which phase applies, before invoking a specialized skill, and to plan and track an end-to-end proteomics analysis.