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bioservices
Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and integrated biological data workflows with BioServices.
bulk-rnaseq
Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff. Use for FASTQ-to-counts analysis, nf-core/rnaseq configuration, STAR/Salmon quantification,…
lamindb
Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations. Use for reproducible biological data curation or a LaminDB lakehouse.
pathway-enrichment
Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enri…
primekg
Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths. Use for PrimeKG reproducibility, biological association lookup, and hypothesis generation with relation and data provenance preserved.
pydeseq2
Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.
scientific-schematics
Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two generations. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
biopython
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.
lamindb
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 data with biological ontologies, building data lakehouses, or …
scientific-schematics
Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
iso10993-evaluator
Biological evaluation planning skill implementing ISO 10993-1 for biocompatibility testing strategy
material-model-library
Biomaterial constitutive model library skill providing validated material properties for biological tissues and implant materials
wastewater-optimization
Specialized skill for biological and physical-chemical wastewater treatment process optimization with activated sludge modeling, nutrient removal, aeration efficiency, and energy minimization.
tooluniverse-spatial-omics-analysis
Spatial multi-omics interpretation pipeline. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into biological insights via domain-by-domain characterization, cell-type composition, spatial gene expression patterns, RNA+protein+metabolite integration. Use for Visium, MERFISH, seqFISH, Slide-seq, spatial proteomics, and spati…
tooluniverse-data-integration-analysis
Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism.
tooluniverse-pathway-disease-genetics
Connect GWAS variants to biological pathways and druggable targets. Maps GWAS hits to causal genes (via fine-mapping/eQTL), then to pathways (Reactome, KEGG, WikiPathways), then to existing drugs hitting those pathways. Use for pathway-level disease mechanisms, druggable-pathway prioritization from GWAS, SNP-to-pathway-to-target tracing, and tissue-specific…
tooluniverse-sequence-analysis
Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, ortholog discovery, and FASTQ QC + alignment workflows (Trimmomatic, BWA, samtools, coverage depth). Use for sequence retrieval, sequence comparison, FASTQ QC analysis, and read alignment pre-processing.
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Sources and import coverage