Local-first CLI for reproducible biological analysis, with provenance tracked on every step.
Skill Claude Code
Verify harness changes at the package boundary — build dist, link the package into a scratch consumer, drive runAgent/tools/gateways against a real Postgres via podman. Use after changing @inflexa-ai/harness when the CLI does not yet consume the change.
Skill Claude CodeCodex
Bulk RNA-seq and microarray differential expression analysis including method selection, batch correction, and complex experimental designs.
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Molecular structure analysis, SAR triage, compound library characterization, QSAR modeling, ADMET prediction, chemical space visualization, target engagement assessment, drug perturbation connectivity scoring, and selectivity profiling.
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Chromatin regulation analysis from called peaks and count matrices — differential binding, signal summarisation, peak annotation, and scATAC-seq.
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DNA methylation analysis — array (450K/EPIC), bisulfite-seq, DMP/DMR detection, clocks, deconvolution, and EWAS.
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Systematic drug repurposing via signature matching, target-based analysis, network proximity, genetic evidence scoring, and clinical evidence mining.
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Functional enrichment and pathway analysis including GSEA, ORA, ssGSEA, GSVA, and decoupler-based activity inference.
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Analysis of called genomic variants — filtering, annotation, GWAS, and population-genetics summaries from VCF and PLINK-format data.
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Immune cell deconvolution, immune signature scoring, checkpoint expression panels, TCR/BCR repertoire analysis, tumor microenvironment characterization, and IO response prediction.
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Metabolomics and lipidomics analysis — untargeted/targeted workflows, normalization, annotation, and pathway mapping.
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Microbiome analysis — compositional data handling, 16S/ITS amplicon, shotgun metagenomics, diversity, differential abundance, and functional profiling.
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Multi-omics integration methods including factor analysis, supervised classification, network fusion, and causal modeling across modalities.
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Multi-modal single-cell analysis for CITE-seq, Multiome, TEA-seq, and DOGMA-seq including joint embedding, per-modality QC, and cross-modal integration.
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Network and regulatory analysis including co-expression networks, GRN inference, PPI analysis, and TF activity scoring.
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Pharmacokinetic/pharmacodynamic modeling, exposure-response analysis, clinical response classification (RECIST/iRECIST), dose-response curves, population PK covariate modeling, PD biomarker tracking, PK-PD hysteresis, and time-to-event endpoints.
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Proteomics analysis covering DDA, DIA, TMT/iTRAQ, Olink, and SomaScan platforms including preprocessing, normalization, differential expression, and PTM analysis.
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Cross-cutting principles for all omics analysis — AnnData/MuData universal containers, Python-first policy, data format detection, analysis phases, and shared analytical methods.
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Single-cell analysis pipeline covering scRNA-seq, snRNA-seq, and CyTOF (mass cytometry) — QC, normalization, integration, clustering, annotation, differential expression, trajectory, cell communication, and TF activity inference.
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Spatial transcriptomics and spatial proteomics analysis covering technology-specific workflows, spatial statistics, deconvolution, and niche analysis.
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Statistical modeling and machine learning for biomarker discovery, survival analysis, classification, regression, and model interpretation.
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Safety pharmacology assessment, CTCAE grading, organ-specific toxicity biomarkers, CYP liability analysis, structural alerts, and drug-drug interaction evaluation.
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: