4,114 skills
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.
Create professional PDF reports with text, tables, and embedded images using reportlab. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
OmicVerse data I/O: use ov.read(), ov.io.read_h5ad, read_10x_h5, read_10x_mtx, read_visium, read_visium_hd, read_nanostring instead of scanpy. Covers h5ad, 10x, spatial, CSV formats.
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
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.
CellFateGenie: Adaptive Threshold Regression for pseudotime-associated gene discovery, Mellon density, lineage scoring via ov.single.Fate.
Daily paper recommendation workflow — search arXiv and Semantic Scholar, score and recommend papers
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
Submit compact STRING API requests for network, interaction partner, and enrichment endpoints. Use when a user wants concise STRING summaries
Fetch GTEx single-tissue eQTL associations from one variant input by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query for the GTEx v2 API. Use when a user wants eQTL associations returned as JSON.
Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries
Submit compact EVA REST requests for species metadata and archived variant lookups. Use when a user wants concise European Variation Archive summaries
Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries
Submit, poll, and summarize NCBI BLAST Common URL API jobs (Blast.cgi) for nucleotide or protein sequences. Use when a user wants RID status, BLAST results, or compact top-hit summaries; fetch raw Text/JSON2 only on request.
Submit compact NCBI PMC Open Access requests for article/file availability metadata. Use when a user wants concise PMC Open Access summaries; save raw XML only on request.
Submit compact RNAcentral API requests for RNA entry browsing, single-entry lookup, and cross-reference retrieval. Use when a user wants concise RNAcentral summaries
Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries
Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries
Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries
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
Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries
Submit compact bioRxiv and medRxiv API requests for details, publication-linkage, and DOI lookups. Use when a user wants concise preprint metadata summaries
Detect Neanderthal and Denisovan introgression segments from modern human genomes
Ancestry decomposition PCA against the Simons Genome Diversity Project
Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.