Best Research Skills for Claude Code

spatial-transcriptomics-tutorials-with-omicverse

@Starlitnightly

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.

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

@Starlitnightly

Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visualisations.

single-cell-annotation-skills-with-omicverse

@Starlitnightly

Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

single-cell-multi-omics-integration

@Starlitnightly

Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.

single-trajectory-analysis

@Starlitnightly

Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.

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

@Starlitnightly

Guide users through OmicVerse plotting utilities showcased in the bulk, color system, and single-cell visualization tutorials, including venn/volcano charts, palette selection, and advanced embedding layouts.

tooluniverse

@jimmc414

Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

venue-templates

@jimmc414

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

clinical-decision-support

@jimmc414

"Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis."

research-lookup

@jimmc414

"Look up current research information using Perplexity's Sonar Pro or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations."