omicclaw

In the author's own words, from each skill's SKILL.md — showing the first 30 of 32 files.

• biocontext-knowledge-queries

  BioContext knowledge: UniProt, AlphaFold, STRING, Reactome, GO, PanglaoDB, PubMed, OpenTargets queries via ov.biocontext for gene annotation.

  src/omicverse_skills/skills/biocontext-knowledge/SKILL.md on GitHub (opens in a new tab)

• bulk-rna-seq-batch-correction-with-combat

  Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.

  src/omicverse_skills/skills/bulk-combat-correction/SKILL.md on GitHub (opens in a new tab)

• bulk-rna-seq-differential-expression-with-omicverse

  Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, volcano plots, and pathway enrichment in OmicVerse.

  src/omicverse_skills/skills/bulk-deg-analysis/SKILL.md on GitHub (opens in a new tab)

• bulk-rna-seq-deseq2-analysis-with-omicverse

  PyDESeq2 differential expression: ID mapping, DE testing, fold-change thresholding, and GSEA enrichment visualization in OmicVerse.

  src/omicverse_skills/skills/bulk-deseq2-analysis/SKILL.md on GitHub (opens in a new tab)

• string-protein-interaction-analysis-with-omicverse

  STRING protein-protein interaction network analysis with pyPPI: query STRING database, build PPI graphs, expand with add_nodes, and visualize styled networks for bulk gene lists.

  src/omicverse_skills/skills/bulk-stringdb-ppi/SKILL.md on GitHub (opens in a new tab)

• bulk-rna-seq-deconvolution-with-bulk2single

  Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.

  src/omicverse_skills/skills/bulk-to-single-deconvolution/SKILL.md on GitHub (opens in a new tab)

• bulktrajblend-trajectory-interpolation

  Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.

  src/omicverse_skills/skills/bulk-trajblend-interpolation/SKILL.md on GitHub (opens in a new tab)

• bulk-wgcna-analysis-with-omicverse

  WGCNA co-expression network: soft-threshold, module detection, eigengenes, hub genes, and trait correlation in OmicVerse.

  src/omicverse_skills/skills/bulk-wgcna-analysis/SKILL.md on GitHub (opens in a new tab)

• data-export-excel

  Export analysis results, data tables, and formatted spreadsheets to Excel files using openpyxl. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

  src/omicverse_skills/skills/data-export-excel/SKILL.md on GitHub (opens in a new tab)

• data-export-pdf

  Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

  src/omicverse_skills/skills/data-export-pdf/SKILL.md on GitHub (opens in a new tab)

• data-io-loading

  OmicVerse data I/O: use ov.read(), ov.io.read_h5ad, read_10x_h5, read_10x_mtx, read_visium, read_visium_hd, read_nanostring instead of scanpy. Covers h5ad, 10x, spatial, CSV formats.

  src/omicverse_skills/skills/data-io-loading/SKILL.md on GitHub (opens in a new tab)

• data-stats-analysis

  Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

  src/omicverse_skills/skills/data-stats-analysis/SKILL.md on GitHub (opens in a new tab)

• data-transform

  Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

  src/omicverse_skills/skills/data-transform/SKILL.md on GitHub (opens in a new tab)

• data-viz-plots

  Publication-quality matplotlib/seaborn plots: scatter, heatmap, violin, bar, line, multi-panel figures. Works with ANY LLM provider.

  src/omicverse_skills/skills/data-viz-plots/SKILL.md on GitHub (opens in a new tab)

• datasets-loading

  OmicVerse built-in datasets: pbmc3k, pancreas, dentategyrus, zebrafish, immune, spatial, multiome, plus create_mock_dataset() and predefined_signatures GMT gene sets.

  src/omicverse_skills/skills/datasets-loading/SKILL.md on GitHub (opens in a new tab)

• fastq-analysis-pipeline

  Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.

  src/omicverse_skills/skills/fastq-analysis/SKILL.md on GitHub (opens in a new tab)

• foundation-model-analysis

  Foundation model workflows: scGPT, Geneformer, UCE, CellPLM cell embedding, annotation, integration via ov.fm unified API. 22 models.

  src/omicverse_skills/skills/fm-foundation-models/SKILL.md on GitHub (opens in a new tab)

• gsea-enrichment-analysis

  Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.

  src/omicverse_skills/skills/gsea-enrichment/SKILL.md on GitHub (opens in a new tab)

• omicverse-visualization-for-bulk-color-systems-and-single-cell-d

  OmicVerse plotting: volcano, venn, boxplot, embedding, density, dotplot, convex hull, stacked bar, and Forbidden City color palettes.

  src/omicverse_skills/skills/plotting-visualization/SKILL.md on GitHub (opens in a new tab)

• single-cell-annotation-skills-with-omicverse

  Cell type annotation: SCSA, MetaTiME, CellVote consensus, CellMatch, GPTAnno, weighted KNN label transfer in OmicVerse.

  src/omicverse_skills/skills/single-annotation/SKILL.md on GitHub (opens in a new tab)

• cellfate-pseudotime-gene-analysis

  CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.

  src/omicverse_skills/skills/single-cellfate-analysis/SKILL.md on GitHub (opens in a new tab)

• single-cell-cellphonedb-communication-mapping

  CellPhoneDB v5 ligand-receptor analysis, cell-cell communication networks, and CellChat-style visualization in OmicVerse.

  src/omicverse_skills/skills/single-cellphone-db/SKILL.md on GitHub (opens in a new tab)

• single-cell-clustering-and-batch-correction-with-omicverse

  Single-cell clustering (Leiden, Louvain, scICE, GMM), batch correction (Harmony, scVI, BBKNN, Combat), topic modeling, and cNMF in OmicVerse.

  src/omicverse_skills/skills/single-clustering/SKILL.md on GitHub (opens in a new tab)

• single-cell-downstream-analysis

  AUCell pathway scoring, metacell DEG, scDrug response, SCENIC regulons, cNMF programs, and NOCD community detection in OmicVerse.

  src/omicverse_skills/skills/single-downstream-analysis/SKILL.md on GitHub (opens in a new tab)

• single-cell-multi-omics-integration

  Multi-omics integration: MOFA factor analysis, GLUE unpaired alignment, SIMBA batch correction, TOSICA label transfer, StaVIA trajectory. Covers scRNA+scATAC paired/unpaired workflows.

  src/omicverse_skills/skills/single-multiomics/SKILL.md on GitHub (opens in a new tab)

• single-popv-annotation

  PopV population-level cell annotation: 10 algorithms (SCVI, SCANVI, CellTypist, OnClass, RF, SVM, XGBoost, BBKNN, HARMONY, SCANORAMA), consensus voting, pretrained hub models.

  src/omicverse_skills/skills/single-popv-annotation/SKILL.md on GitHub (opens in a new tab)

• single-cell-preprocessing-with-omicverse

  Single-cell QC, normalization, HVG detection, PCA, neighbor graph, UMAP/tSNE embedding pipelines in OmicVerse (CPU/GPU).

  src/omicverse_skills/skills/single-preprocessing/SKILL.md on GitHub (opens in a new tab)

• scenic-gene-regulatory-network

  SCENIC gene regulatory network: RegDiffusion GRN inference, cisTarget regulon pruning, AUCell scoring, RSS, regulon embeddings in OmicVerse.

  src/omicverse_skills/skills/single-scenic-grn/SKILL.md on GitHub (opens in a new tab)

• single2spatial-spatial-mapping

  Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

  src/omicverse_skills/skills/single-to-spatial-mapping/SKILL.md on GitHub (opens in a new tab)

• single-trajectory-analysis

  Trajectory & RNA velocity: PAGA, Palantir, VIA, dynamo, scVelo, latentvelo, graphvelo backends via ov.single.Velo. Pseudotime, stream plots.

  src/omicverse_skills/skills/single-trajectory/SKILL.md on GitHub (opens in a new tab)

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