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Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.
Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.
Generates complete tumor immune-infiltration-guided bulk-transcriptome diagnostic biomarker and machine-learning research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on di...
Designs QTL colocalization studies that connect eQTL, pQTL, sQTL, or related molecular QTL signals with GWAS loci. Always use this skill whenever a user wants to plan, scope, or structure a locus-level study asking whether a GWAS association and a molecular QTL association may reflect the same un...
Use when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk distribution plots, heatmap, and time-dependent ROC curves. NOT for: model training, feature selection, nomogram construction, c...
Use biotech-pitch-deck-narrative for academic writing workflows that need structured investor-facing storytelling, explicit assumptions, and clear output boundaries.
Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for systematic review and meta-analysis. Handles both database lookup by PMID and real-time LLM extraction.
Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.
Access ChEA3 and Harmonizome ChEA data for transcription factor enrichment analysis and metadata retrieval. Use when the user needs to perform ChEA3 enrichment analysis on a gene set, get metadata about the ChEA dataset, or retrieve information about a specific transcription factor (attribute).
Retrieves comprehensive gene information including PubMed publication counts, NCBI summaries, and Ensembl transcript data. Supports batch processing and file input. Invoke when the user asks for gene details, publication statistics, or needs to analyze a list of genes.
Use when analyzing biotech patent landscapes, identifying white spaces in pharmaceutical IP, tracking competitor patents, or assessing freedom to operate for drug development. Provides comprehensive patent analysis and strategic insights for life sciences innovation.
Analyze data with `metagenomic-krona-chart` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
Generate Baujat plots for heterogeneity analysis. Identify studies that contribute most to the overall meta-analysis results and heterogeneity, helping discover potential outlier studies. Input meta-analysis data CSV, output Baujat plot PNG and contribution data CSV.
Generate meta-analysis forest plots for binary classification data. Input is a CSV file containing study names, event counts and sample sizes for experimental and control groups. Output includes forest plot PNG and data table CSV.
Generate Meta-analysis funnel plots and perform publication bias testing. Takes CSV file with Meta-analysis data as input, outputs funnel plot PNG, Egger test and Begg test results.
Generate radial plots (Radial Plot/Galbraith Plot) for heterogeneity analysis. Visually assess heterogeneity across studies by displaying the relationship between standardized effect sizes and precision. Input: Meta-analysis data in CSV format; Output: Radial plot PNG and data CSV.
Generate publication-quality sequence logos for DNA or protein motifs.
Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.
Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.
Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.
Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
Score the novelty of biological targets through literature mining and.
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