GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
☆ 18,943View skill
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Categories: documentation scientific computing
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GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 18,943View skill
GitHub
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct...
☆ 18,938View skill
GitHub
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway an...
☆ 18,938View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 8,603View skill
GitHub
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
☆ 8,603View skill
GitHub
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway an...
☆ 8,603View skill
GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
☆ 8,603View skill
GitHub
bio-metabolomics-pathway-mapping
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathway...
☆ 300View skill
GitHub
bio-pathway-reactome
Reactome pathway enrichment using ReactomePA package. Performs over-representation analysis and GSEA on Reactome pathways, a curated peer-reviewed knowledgebase of biological pathways. Supports visualization an...
☆ 299View skill
GitHub
bio-workflows-expression-to-pathways
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
☆ 299View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 283View skill
GitHub
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct...
☆ 26View skill
GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
☆ 26View skill
GitHub
numerical-stability
Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diagnosing numerical blow-up, checking CFL/Fourier criteria, von Ne...
☆ 21View skill
GitHub
materials-properties
Expert assistant for calculating materials properties from first-principles using ASE - structure relaxation, surface energies, adsorption, reaction barriers, phonons, elastic constants, and thermodynamic model...
☆ 14View skill
GitHub
gcell-pathway
Pathway enrichment analysis using gcell. Use this skill when users ask about: - Gene set enrichment analysis - GO (Gene Ontology) enrichment - KEGG pathway analysis - Reactome pathway enrichment - Custom pathwa...
☆ 12View skill
GitHub
crn-topology
Chemical Reaction Network topology for generating and analyzing reaction
☆ 5View skill
GitHub
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway an...
☆ 3View skill
GitHub
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
☆ 3View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 3View skill
GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
☆ 3View skill
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