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Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.
Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.
Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.
A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML, reference sequence verification, or fragment processing.
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating ...
Use when analyzing transcription factor (TF) regulatory networks using Dorothea database. Input gene list, identify regulating transcription factors, generate TF-Target network visualization. For: transcription factor enrichment analysis, gene regulatory network research.
Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. NOT for single-cell RNA-seq, methylation data, or non-expression data.
Generate leave-one-out sensitivity analysis plots for meta-analysis. Input is a CSV file containing meta-analysis data; outputs are a sensitivity forest plot (PNG) and a sensitivity data table (CSV) showing pooled effect estimates after excluding each study in turn.
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...
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Use biotech-pitch-deck-narrative for academic writing workflows that need structured investor-facing storytelling, explicit assumptions, and clear output boundaries.
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
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.
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