UC Davis Proteomics Core pipeline — end-to-end proteomics search + differential expression from raw .raw/.d/.mzML files (DIA-NN / Sage, limpa/limma). Auto-installs its toolchain, derives search parameters from the data type, writes a biological analysis report and a full reproducibility bundle, and packages results into tidy session folders.
Plugin ucdavis-proteomics-core-pipeline from marketplace ucdavis-proteomics-core in bsphinney/DE-LIMP. Commands read from the repo's manifest — yesterday.
This plugin runs code on your machine — its hooks fire automatically on events like tool use. The exact commands are listed below; read them before installing.
ucdavis-proteomics-core-pipelineRun a proteomics search and/or differential expression analysis from mass-spec data. Use this whenever the user wants to "analyze my proteomics data", "search these raw files", "run my DIA/DDA data", "find differentially expressed proteins", "process this timsTOF/Astral/Orbitrap run", or points at a
python3 "${CLAUDE_PLUGIN_ROOT}/scripts/transcript_hook.py" || python "${CLAUDE_PLUGIN_ROOT}/scripts/transcript_hook.py"
python3 "${CLAUDE_PLUGIN_ROOT}/scripts/transcript_hook.py" || python "${CLAUDE_PLUGIN_ROOT}/scripts/transcript_hook.py"
SANDBOX copy of the UC Davis Proteomics Core pipeline (forked from stable v2.4.3). For developing new capability -- phosphosite analysis and the DE-LIMP visualisations -- without risking the skill that runs real searches. Not for production analyses.
1 skill
General life-sciences research workflows with query routing, evidence synthesis, and optional parallel subagent analysis across genetics, omics, biology, chemistry, structure, clinical evidence, and public dataset discovery.
50 skills
100+ bioinformatics Agent Skills: pharmacogenomics, clinical variant interpretation, GWAS and PRS, ancestry, RNA-seq and single-cell, metagenomics, proteomics, methylation clocks, nf-core pipeline wrappers. Many run deterministically from the CLI with demo data and write a reproducibility bundle. Local-first, privacy-focused.
111 skills · 4 commands
197 validated life sciences skills — genomics, proteomics, drug discovery, biostatistics, scientific computing
200 skills
Spatial proteomics analysis toolchain (MCMICRO pipeline) exposed as MCP tools for Claude Code.
1 MCP server
Genomics, single-cell, proteomics, neuroscience and systems biology.
200 skills
Genomics, proteomics, and single-cell analysis (Scanpy, BioPython, pysam, ESM) (38 skills)
38 skills
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