Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper.
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Skill Claude CodeCodex
Load when summarising functional impact of an annotated variant CSV — per-IMPACT counts (HIGH / MODERATE / LOW / MODIFIER), top consequences, gene-affected count. Skip when input is a raw VCF (convert with bcftools +split-vep first); calling raw variants (use genomics-variant-calling); filtering VCFs (use…
Skill Claude CodeCodex
Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split). Skip when filtering / merging VCFs (use genomics-vcf-operations); calling structural variants (use genomics-sv-detection); adding functional…
Skill Claude CodeCodex
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when the input is a BAM (use genomics-variant-calling); adding functional annotations (use genomics-variant-annotation).
Skill Claude CodeCodex
Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand; only routing a query (use orchestrator).
Skill Claude CodeCodex
Load when annotating LC-MS features against a built-in 15-metabolite HMDB demo dictionary by m/z within a --ppm tolerance — emits a per-feature annotation table. Skip when needing real HMDB / KEGG / LipidMaps / METLIN look-up (this skill is demo-only); raw spectra (use metabolomics-xcms-preprocessing).
Skill Claude CodeCodex
Load when running two-group metabolomics DE (t-test + log2FC + BH-FDR + PCA) on a feature × sample CSV using --group-a-prefix / --group-b-prefix (default ctrl / treat). Skip when needing tunable test backends (use metabolomics-statistics); raw spectra.
Skill Claude CodeCodex
Load when normalising a feature × sample metabolomics CSV via median, quantile, total (sum), PQN (probabilistic quotient), or log methods — emits a normalised wide-form table. Skip when also imputing (use metabolomics-quantification); raw spectra (use metabolomics-xcms-preprocessing).
Skill Claude CodeCodex
Load when running over-representation analysis (ORA) on a metabolite list via Fisher's exact test against a built-in 9-pathway DEMO dictionary, BH-FDR adjusted. Skip when needing real KEGG / Reactome (this skill is demo-only); mummichog / fella topology methods (CLI accepts them but only ORA runs).
Skill Claude CodeCodex
Load when running per-sample peak picking on a feature × intensity table via scipy.signal.findpeaks — emits per-(sample, feature) detected peaks with prominence and width. Skip when working with mz / RT raw scans (use metabolomics-xcms-preprocessing); only normalising / quantifying (use metabolomics-quantification).
Skill Claude CodeCodex
Load when imputing missing values (min / median / KNN) and normalising (TIC / median / log) a feature × sample metabolomics CSV. Skip when only normalisation is needed (use metabolomics-normalization); the input is raw spectra (use metabolomics-xcms-preprocessing).
Skill Claude CodeCodex
Load when running univariate two-group testing (t-test / Wilcoxon / ANOVA / Kruskal-Wallis) on a feature × sample metabolomics CSV with --group1-prefix / --group2-prefix column matching, BH-FDR adjusted. Skip when working with raw spectra (use metabolomics-xcms-preprocessing); two-group DE with default ctrl / treat…
Skill Claude CodeCodex
Load when running an XCMS-style preprocessing summary on LC-MS metabolomics raw / vendor-converted files — emits a peak table with m/z, retention time, and per-sample intensities. Skip when working with an already-built peak table (use metabolomics-peak-detection); only annotation is needed (use…
Skill Claude CodeCodex
Load when routing a natural-language omics query to the correct domain skill across spatial / singlecell / genomics / proteomics / metabolomics / bulkrna domains via keyword / LLM / hybrid matching. Skip when the target skill is already known — invoke that skill directly.
Skill Claude CodeCodex
Load when scaffolding a NEW OmicsClaw skill from a natural-language request — generates the skill directory layout (skill.yaml, SKILL.md, references/, tests/) under the chosen domain. Skip when modifying an existing skill (edit its files directly); only routing a query (use orchestrator).
Skill Claude CodeCodex
Load when ingesting a MaxQuant proteinGroups.txt, FragPipe combinedprotein.tsv, DIA-NN report, or generic CSV / TSV protein-quantification table — normalises columns to a standard schema, emits tables/proteins.csv. Skip when raw spectra are the input (run the search engine first); the file is already OmicsClaw schema.
Skill Claude CodeCodex
Load when computing two-group differential protein abundance (group2 vs group1, log2FC + p-value + BH-adjusted FDR) via Welch t-test, equal-variance t-test, or Mann-Whitney on a wide protein × sample CSV. Skip when you need multi-condition DE (run pairwise contrasts manually); label-based TMT linear-mixed models.
Skill Claude CodeCodex
Load when running over-representation analysis (ORA) on a list of proteins via Fisher's exact test against a built-in 8-pathway DEMO dictionary, with BH-FDR correction. Skip when needing a real pathway database (this skill is demo-only) (use bulkrna-enrichment); rank-based GSEA.
Skill Claude CodeCodex
Load when summarising peptide identifications (PSM count, unique peptide count, distinct protein count, score / charge distributions) from a peptide-level CSV produced by MaxQuant / FragPipe / DIA-NN. Skip when raw spectra are the input (run a search engine first); working with protein-quantification tables (use…
Skill Claude CodeCodex
Load when computing protein-table QC — proteins × samples count, missing-value rate, intensity CV (median + mean) — from a MaxQuant / FragPipe / DIA-NN protein-quantification CSV. Skip when raw mzML / RAW spectra are the input (run a search engine first); peptide-level QC is needed (use proteomics-identification).
Skill Claude CodeCodex
Load when summarising PTM sites (phosphorylation, acetylation, ubiquitination, etc.) from a per-site CSV — site-class assignment (Olsen et al. Class I/II/III by localizationprobability), per-PTM-type counts, amino-acid distribution, sites-per-protein. Skip when raw spectra are the input; you only need protein-level…
Skill Claude CodeCodex
Load when computing per-protein abundance from a peptide / PSM table via LFQ (intensity summation), iBAQ (intensity / tryptic peptide count), or spectral counting (PSMs per protein). Skip when the input is already protein-level (use proteomics-ms-qc); label-based TMT / iTRAQ workflows (search upstream first).
Skill Claude CodeCodex
Load when summarising cross-linking MS (XL-MS) results — intra/inter-protein link split, optional FDR filtering, distance-constraint validation against a per-crosslinker (DSS / BS3 / EDC / DSSO / DSBU) max distance. Skip when raw spectra are the input (run XlinkX / pLink / xiSEARCH first); no XL-MS experiment was…
Skill Claude CodeCodex
Load when preprocessing a single-cell ATAC peak × cell AnnData via Signac-style TF-IDF + LSI + Leiden, producing a clustered UMAP-ready object. Skip when input is fragments; BAM (peak calling not implemented here); scRNA preprocessing (use sc-preprocessing).
Skill Claude CodeCodex
Load when removing ambient RNA contamination from droplet-based scRNA-seq using a simple subtraction path, CellBender, or SoupX. Skip when the contamination is multiplet barcodes (use sc-doublet-detection); before counts exist (use sc-count).
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: