Research

--> --- name: bio-genomics-variant-calling description: Germline and somatic variant calling (SNVs, Indels) using GATK HaplotypeCaller, Mutect2, DeepVariant, or FreeBayes. Includes GVCF workflow, VQSR, and hard filtering. tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Germline and somatic small variant calling (SNVs, Indels). Supports GATK HaplotypeCaller, M...

--> --- name: bio-genomics-cnv-calling description: Copy number variant detection from exome/WGS data using CNVkit, Control-FREEC, or GATK gCNV. Supports tumor-normal pairs, tumor-only, and germline modes. tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Detect copy number variants from targeted/exome/WGS sequencing data.

--> --- name: bio-sc-doublet-detection description: Doublet detection and removal using Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering. tool_type: mixed primary_tool: singlecell measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Detect and remove doublets (multiple cells captured in one droplet) from scRNA-seq data. Essential QC step before clustering.

--> --- name: bio-sc-cell-annotation description: Automated cell type annotation using marker genes, CellTypist, SingleR, or scmap. Supports custom references and marker gene lists. tool_type: mixed primary_tool: singlecell measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- You are **SC Annotate**, a specialised OmicsClaw agent for automated cell type annotation in single-cell data. Your role is to as...

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'precision-grounded-variant-summarization' description: 'Produce evidence-grounded genetic variant summaries with provenance, conflict handling, and hallucination controls.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

--> --- name: 'notion-research-documentation' description: 'Searches across your Notion workspace, synthesizes findings from multiple pages, and creates comprehensive research documentation saved as new Notion pages. Turns scattered information into structured reports with proper citations and actionable insights.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Enables comprehensive research workf...

Load when estimating RNA velocity on a spatial AnnData with `layers["spliced"]` + `layers["unspliced"]` via scVelo (stochastic / deterministic / dynamical) or veloVI (deep generative). Skip when input lacks the spliced/unspliced layers (must be quantified upstream by velocyto / kb-python / STARsolo) or for non-spatial scRNA velocity (use `sc-velocity`).

Load when ranking spatial cluster markers or comparing two spatial groups in spatial transcriptomics. Skip if the data is single-cell (use sc-de) or bulk (use bulkrna-de), or for spatially variable expression discovery (use spatial-genes).

Load when computing ligand-receptor cell-cell communication on a preprocessed spatial AnnData with `obs[cell_type_key]` (default `leiden`) via LIANA (default), CellPhoneDB, FastCCC, or CellChat (R). Skip when running scRNA-only L-R inference (use `sc-cell-communication`) or when no cell-type labels exist (run `spatial-annotate` or `spatial-domains` first).

Load when an external single-cell h5ad/h5/loom/mtx needs to be canonicalised onto the OmicsClaw AnnData contract before downstream scRNA skills run. Skip when data already came from sc-count (already canonical), or for bulk RNA-seq (use bulkrna-qc) or spatial (use spatial-preprocess).

Load when computing per-cell QC metrics (n_genes, total counts, mt%, ribo%) on a single-cell AnnData before filtering. Skip when reads are still raw FASTQ (use sc-fastq-qc) or you want to filter cells now (use sc-filter).

Load when normalising QC'd scRNA into a PCA-ready AnnData via scanpy / Seurat / SCTransform / Pearson residuals. Skip when QC thresholds are still undecided (use sc-qc) or for batch correction across samples (use sc-batch-integration).

Load when computing per-cell pathway / gene-set scores on a normalised scRNA AnnData via AUCell (R or Python) or Scanpy score_genes. Skip when running condition-vs-control bulk-style enrichment on top of a DE table (use sc-enrichment) or for de-novo gene-program discovery (use sc-gene-programs).

Load when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy Wilcoxon / t-test / logreg or COSG specificity. Skip when comparing condition-vs-control with replicates (use sc-de) or for assigning cell-type labels (use sc-cell-annotation).

Load when extracting gene programs (NMF / cNMF factorisation) and per-cell program usage scores from a non-negative scRNA AnnData. Skip when ranking marker genes per cluster (use sc-markers) or for inferring TF → target regulons (use sc-grn).

Load when finding marker genes per cluster or comparing condition expression in single-cell RNA-seq. Skip if the data is bulk (use bulkrna-de) or spatial (use spatial-de), or for cluster-only markers without conditions (use sc-markers).

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` for QC) or for label-based TMT / iTRAQ workflows (search upstream first).

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 or when only routing a query (use `orchestrator`).

Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use `genomics-alignment`) or when peak / variant files are the input (use the relevant downstream skill).

Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a SAM or BAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2). Skip when running the alignment step itself or when only FASTQ-level QC is needed (use `genomics-qc`).

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE. Skip if data is raw FASTQ (use bulkrna-read-qc) or aligner logs (use bulkrna-read-alignment), or for single-cell counts (use sc-qc).

Load when querying STRING for the protein-protein interaction subgraph induced by a bulk RNA-seq DEG list and finding hub genes. Skip for pathway enrichment of the same list (use bulkrna-enrichment) or for de novo co-expression network discovery (use bulkrna-coexpression).

Load when discovering gene co-expression modules and hub genes in a bulk RNA-seq cohort via WGCNA-style soft-thresholded networks. Skip for direct DE comparison (use bulkrna-de) or PPI lookup of an existing gene list (use bulkrna-ppi-network); single-cell co-expression uses sc-grn instead.

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'chromfound-scatac-foundation-model' description: 'Apply ChromFound, a genome-wide foundation model for single-cell chromatin accessibility (scATAC-seq), to enable cell-type annotation, regulatory element discovery, and cross-tissue transfer.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---