GitHub
single-cell-cellphonedb-communication-mapping
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
☆ 834View skill
documentation scientific computing AI Skills
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GitHub
single-cell-clustering-and-batch-correction-with-omicverse
Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_s...
☆ 834View skill
GitHub
single-cell-annotation-skills-with-omicverse
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
☆ 834View skill
GitHub
single-cell-downstream-analysis
Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.
☆ 834View skill
GitHub
mesh-analysis
Analyzes 3D mesh files (STL) to calculate geometric properties (volume, components) and extract attribute data. Use this skill to process noisy 3D scan data and filter debris.
☆ 591View skill
GitHub
research-synthesis-workflow
A step-by-step guide to synthesizing research from multiple sources into a coherent summary.
☆ 552View skill
GitHub
deep-researcher
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources.
☆ 552View skill
GitHub
hypothesis-generation
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
☆ 441View skill
GitHub
tooluniverse
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+...
☆ 441View skill
GitHub
research-lookup
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...
☆ 441View skill
GitHub
skill-researcher
Conduct general research using web search, documentation, and codebase exploration. Invoke for non-Lean research tasks.
☆ 431View skill
GitHub
ark-research
Research technical solutions by searching the web, examining GitHub repos, and gathering evidence. Use when exploring implementation options or evaluating technologies.
☆ 319View skill
GitHub
business-analytics-reporter
This skill should be used when analyzing business sales and revenue data from CSV files to identify weak areas, generate statistical insights, and provide strategic improvement recommendations. Use when the use...
☆ 315View skill
GitHub
bio-flow-cytometry-fcs-handling
Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
☆ 300View skill
GitHub
bio-pathway-gsea
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Uses a ranked gene list to find coordinated changes in gene sets without requiring arbitrary significance cutoffs. Detects subtle but coordi...
☆ 300View skill
GitHub
bio-transcription-translation
Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.
☆ 300View skill
GitHub
bio-alignment-msa-parsing
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis.
☆ 300View skill
GitHub
bio-population-genetics-linkage-disequilibrium
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow.
☆ 300View skill
GitHub
bio-proteomics-data-import
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Handles common preprocessing steps like contaminant filtering and missing va...
☆ 300View skill
GitHub
bio-pathway-wikipathways
WikiPathways enrichment using clusterProfiler and rWikiPathways. Performs over-representation analysis and GSEA on community-curated biological pathways. WikiPathways is an open, collaborative platform with pat...
☆ 300View skill
GitHub
bio-spatial-transcriptomics-spatial-statistics
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment.
☆ 300View skill
GitHub
bio-rna-quantification-alignment-free-quant
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use for fast, accurate transcript-level quantification directly from FASTQ files without genome alignment.
☆ 300View skill
GitHub
bio-metabolomics-pathway-mapping
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathway...
☆ 300View skill
GitHub
bio-read-alignment-bwa-alignment
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use for whole genome sequencing, exome sequencing, and ChIP-seq alignment.
☆ 300View skill
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