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Bioinformatics

Genomics and biological data.

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bioinformatics
950

tooluniverse-phylogenetics

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nexus/Newick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-polygenic-risk-score

Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses disease predisposition across conditions including type 2 diabetes, coronary artery disease, and Alzheimer's disease. Use when asked to calculate polygenic risk scores, interpret genetic risk for complex diseases, build custom PRS from GWAS data, or answer questions like "What is my genetic predisposition to breast cancer?"

wu-yc
wu-yc
research
open
bioinformatics
950

protein-interaction-network-analysis

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.

wu-yc
wu-yc
research
open
bioinformatics
946

power-flow-data

Power system network data formats and topology. Use when parsing bus, generator, and branch data for power flow analysis.

benchflow-ai
benchflow-ai
research
open
bioinformatics
946

openai-vision

Analyze images and multi-frame sequences using OpenAI GPT vision models

benchflow-ai
benchflow-ai
research
open
bioinformatics
946

gpt-multimodal

Analyze images and multi-frame sequences using OpenAI GPT series

benchflow-ai
benchflow-ai
research
open
bioinformatics
943

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.

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

gsea-enrichment-analysis

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

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

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.

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

bulk-wgcna-analysis-with-omicverse

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

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

biocontext-knowledge-queries

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

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

foundation-model-analysis

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

Starlitnightly
Starlitnightly
research
open
bioinformatics
943

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.

Starlitnightly
Starlitnightly
research
open
bioinformatics
893

data-analysis

End-to-end R data analysis workflow from exploration through regression to publication-ready tables and figures

pedrohcgs
pedrohcgs
research
open
bioinformatics
848

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.

Prismer-AI
Prismer-AI
research
open
bioinformatics
841

init-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).

OpenLAIR
OpenLAIR
research
open
bioinformatics
785

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.

wuyoscar
wuyoscar
research
open
bioinformatics
785

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.

wuyoscar
wuyoscar
research
open
bioinformatics
785

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.

wuyoscar
wuyoscar
research
open
bioinformatics
785

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.

wuyoscar
wuyoscar
research
open
bioinformatics
785

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.

wuyoscar
wuyoscar
research
open
bioinformatics
771

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.

xjtulyc
xjtulyc
research
open
bioinformatics
759

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

openai
openai
research
open
bioinformatics
759

gnomad-graphql-skill

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

openai
openai
research
open
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