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Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.
Build, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/kinetic laws, species, rules, FBC extension for flux balance, conversion. Interoperates with COBRApy, Tellurium/RoadRunner, COPASI. Use when programmatically constructing ODE or con...
Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significa...
Search KEGG database for gene information to retrieve pathway associations, functional annotations, and disease links.
Analyze protein-protein interaction enrichment using STRING database to identify functional networks and pathway associations.
Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments
Search 78 public scientific, biomedical, materials science, and economic databases via their REST APIs and return structured JSON results. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD, Exoplanet Archive), earth/environment (USGS, NOAA, EPA, OpenWeatherMap), chemistry/drugs (PubChem, ChEMBL,...
Detect Neanderthal and Denisovan introgression segments from modern human genomes
scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
Deterministic CRISPR screen hit ranking from local guide-level count tables
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into
Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession, chromosome, start, end. Output: harmonised TS...
Medical biostatistics hypothesis testing toolkit: t-tests, ANOVA, chi-square, Fisher exact, Mann-Whitney, Kruskal-Wallis, sample size calculation, power analysis, multiple testing correction, survival analysis, and clinical trial biostatistics.
Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
Multi-agent system for biomedical literature review and synthesis
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional two-group contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
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