bioinformatics
185
food-journal-database
Describes the structure of the Food Journal database that allows to store and read food journal entries
majiayu000
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
bioinformatics
185
gene-set-enrichment
Perform gene set enrichment analysis using AI research providers. Analyzes lists of genes to identify biological themes, pathways, and functional associations.
majiayu000
research
bioinformatics
185
curate-bulk-rnaseq
Process bulk RNA-seq datasets for VEuPathDB resources
majiayu000
research
bioinformatics
185
data-model-reporter
Standards for generating Model Cards from data analysis notebooks. Aligned with Hugging Face and ISO transparency standards.
majiayu000
research
bioinformatics
185
end-reason
Oxford Nanopore read end reason QC analysis. Use when analyzing nanopore sequencing quality, checking for adaptive sampling efficiency, investigating read termination patterns, diagnosing sequencing issues, or running QC on POD5/Fast5 data. Integrates with ont-experiments for provenance tracking via Pattern B orchestration. Supports signal_positive, unblock_mux_change, data_service_unblock_mux_change analysis with quality thresholds.
majiayu000
research
bioinformatics
185
hashing-techniques
Hash-based data structures and techniques including frequency counting, duplicate detection, and LRU cache implementation.
majiayu000
research
bioinformatics
172
self-consistency
Sample multiple paths, select most consistent - +17.9% on GSM8K
Miosa-osa
research
bioinformatics
169
swiftdata-inheritance
SwiftData class inheritance patterns for hierarchical models with type-based querying, polymorphic relationships, and when to choose inheritance vs enums. Use when designing SwiftData model hierarchies.
rshankras
research
bioinformatics
165
network-analysis
Analyze network structures, identify communities, measure centrality, and visualize relationships for social networks and organizational structures
aj-geddes
research
bioinformatics
163
sragent
Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. Supports accession conversion (GSE→SRX→SRR), BigQuery metadata queries, manuscript downloads from multiple sources, and scRNA-seq technology identification. Use when working with SRA/GEO datasets, finding publications, or analyzing single-cell sequencing experiments.
ArcInstitute
research
bioinformatics
157
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
Microck
research
bioinformatics
157
gene-therapy-target
Gene Therapy Target Analysis - Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence. Use this skill for gene therapy tasks involving get gene metadata by gene name get vep hgvs Protein structure prediction ESMFold clinvar search. Combines 4 tools from 4 SCP server(s).
InternScience
research
bioinformatics
157
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
Microck
research
bioinformatics
157
gene-disease-association
Gene-Disease Association Analysis - Analyze gene-disease associations: NCBI gene metadata, OpenTargets disease associations, TCGA expression, and Monarch phenotypes. Use this skill for medical genetics tasks involving get gene metadata by gene name get associated targets by disease efoId get gene expression across cancers get joint associated diseases by HPO ID list. Combines 4 tools from 4 SCP server(s).
InternScience
research
bioinformatics
157
gene-expression-atlas
Gene Expression Atlas - Build gene expression atlas: TCGA cancer expression, NCBI gene info, Ensembl gene details, and literature search. Use this skill for transcriptomics tasks involving get gene expression across cancers get gene metadata by gene name get lookup symbol search literature. Combines 4 tools from 4 SCP server(s).
InternScience
research
bioinformatics
157
epigenomic-landscape
Epigenomic Landscape Mapping - Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links. Use this skill for epigenomics tasks involving get overlap region get phenotype region get species binding matrix get track data. Combines 4 tools from 2 SCP server(s).
InternScience
research
bioinformatics
157
gene-family-evolution
Gene Family Evolution Analysis - Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. Use this skill for molecular evolution tasks involving get cafe genetree member symbol get homology symbol get genetree member symbol get taxonomy classification. Combines 4 tools from 1 SCP server(s).
InternScience
research
bioinformatics
157
genetic-counseling-report
Genetic Counseling Variant Report - Generate variant report for genetic counseling: VEP, ClinVar, gene phenotype, and literature evidence. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get phenotype gene pubmed search. Combines 4 tools from 2 SCP server(s).
InternScience
research
bioinformatics
157
comprehensive-variant-annotation
Given an rsID, query multiple databases (dbSNP, FAVOR, GWAS Catalog, ClinVar, gnomAD, PharmGKB, ClinGen) for comprehensive annotation. Use when user asks a general question about a variant without specifying which aspect.
InternScience
research
bioinformatics
157
ensembl-sequence-retrieval
Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.
InternScience
research