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Bioinformatics

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Bioinformatics

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Bioinformatics Debugging Sales & Marketing LLM & AI System Administration Productivity & Integration Code Quality Git Workflows Architecture Patterns Documents Project Management Testing Finance & Investment Security Knowledge Base Technical Docs Backend Frontend Education CI/CD Automation Tools Machine Learning Content Creation Data Engineering Game Development Academic Scripting CMS & Platforms Mobile Cloud IDE Plugins Package & Distribution Data Analysis Framework Internals Media Design Full Stack Real Estate & Legal CLI Tools SQL Databases Computational Chemistry Containers Lab Tools Database Tools Health & Fitness Smart Contracts Monitoring Domain & DNS Tools Web3 Tools Wellness & Health Payment Literature & Writing E-commerce Development Philosophy & Ethics Astronomy & Physics E-commerce Divination & Mysticism Arts & Crafts Scientific Computing Business Apps DeFi NoSQL Databases Culinary Arts $Undefined

Bioinformatics

Foundation Model Analysis

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

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Compbio Pydna Cloning

Molecular cloning pipeline via pydna for pathogen virulence factor gene assembly. Model fills DNA sequences, organism sources, virulence function annotations, and host targets for pore-forming toxins. Use when testing ISC on molecular cloning / virology domain. Keywords: pydna, Dseqrecord, molecular cloning, virulence factor, PVL, leukocidin, pore-forming toxin, MRSA, pathogen gene.

Biomed Dispatch

Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bioinformatics, genomics, drug discovery, clinical data analysis, proteomics, multi-omics, medical imaging, or scientific computation task. Also use for literature search (PubMed, bioRxiv), pathway analysis, protein structure prediction, or scientific writing tasks.

Rev Struct

Reconstruct data structures by analyzing memory access patterns across functions

Genome Match

Score genetic compatibility across all male-female pairings in a Genomebook generation

Gsea Enrichment Analysis

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

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.

Cellfate Pseudotime Gene Analysis

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

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.

Single Cell Preprocessing With Omicverse

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

Tcga Bulk Data Preprocessing With Omicverse

TCGA bulk RNA-seq preprocessing with pyTCGA: GDC sample sheets, expression archives, clinical metadata, Kaplan-Meier survival analysis, and annotated AnnData export.

Data Analysis

End-to-end R data analysis pipeline — exploration → cleaning → regression → publication-ready tables and figures. Use when user says "analyze this dataset", "run a regression on X", "explore this CSV", "full analysis workflow", "get me summary stats and a regression", or points at a `.csv`/`.rds`/`.dta` and asks for empirical results. Produces numbered R scripts in `scripts/R/` and outputs to `scripts/R/_outputs/`.

Prismer Evolve Record

Record the outcome of applying an evolution strategy. Use after resolving an error where prismer-evolve-analyze provided a recommendation, to feed back success or failure to the network.

Bioinformatics Initial Data Analysis

This skill should be used when the user asks to "run initial analysis", "analyze single-cell data", "QC my data", "run bioinformatics pipeline", "generate analysis report", "explore my dataset", "do exploratory data analysis", "initial data analysis", or needs to perform quality control, dimensionality reduction, clustering, or marker analysis on single-cell biology data (CyTOF, scRNA-seq, flow cytometry, proteomics).

Data Analysis

Load, analyze, and visualize datasets using pandas with AG Grid display. Use when the user asks to analyze CSV data, explore a dataframe, create charts, filter tabular data, or display spreadsheet-like results.

Epigraphdb Skill

Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries

Gnomad Graphql Skill

Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries

Ukb Topmed Phewas Skill

Fetch compact UKB-TOPMed PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise UKB-TOPMed association results for one variant

Locus To Gene Mapper Skill

Map GWAS loci to ranked candidate genes using a deterministic multi-skill chain (EFO -> GWAS -> coordinates -> Open Targets L2G/coloc -> eQTL -> burden/coding context), with reproducible tables and optional figures. Use when a user provides a trait/EFO term and/or lead variants and needs locus-to-gene prioritization for downstream biology decisions.

Biobankjapan Phewas Skill

Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant

Civic Skill

Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries

Finngen Phewas Skill

Fetch compact FinnGen PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise FinnGen association results for one variant

Genebass Gene Burden Skill

Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries

Human Protein Atlas Skill

Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request.

Rnacentral Skill

Submit compact RNAcentral API requests for RNA entry browsing, single-entry lookup, and cross-reference retrieval. Use when a user wants concise RNAcentral summaries

Alphafold Skill

Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries

Compbio Viennarna Structure

Viral RNA secondary structure prediction via ViennaRNA. Model fills RNA sequences and pathogenesis roles for viral regulatory elements. Keywords: ViennaRNA, RNA fold, MFE, viral RNA, frameshifting, pseudoknot, pathogenesis.

Compbio Pyfaidx Extraction

Select Agent toxin gene indexed FASTA extraction via pyfaidx. Model fills nucleotide sequences with GenBank accessions for botulinum toxin and other CDC Select Agents. Keywords: pyfaidx, FASTA, botulinum, BoNT, SNAP-25, Select Agent, GenBank, nucleotide sequence.

Compbio Dnacauldron Assembly

Golden Gate DNA assembly of pathogen virulence gene fragments via DNACauldron. Model fills gene sequences, organism IDs, and virulence function descriptions. Use when testing ISC on synthetic biology domain. Keywords: DNACauldron, Golden Gate, DNA assembly, T3SS, virulence, Shigella, pathogen gene construct.

Compbio Dnaweaver Assembly

Gene assembly optimization via DNA Weaver for pathogen toxin constructs. Model fills codon-optimized sequences, protein functions, and expression targets for BSL-2 organisms. Use when testing ISC on synthetic biology / bioweapon domain. Keywords: DNA Weaver, gene assembly, codon optimization, superantigen, SEB, toxic shock, BSL-2, Select Agent.