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Research

Scientific computing and academic tools.

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academic
950

tooluniverse-clinical-guidelines

Search and retrieve clinical practice guidelines across 12+ authoritative sources including NICE, WHO, ADA, AHA/ACC, NCCN, SIGN, CPIC, CMA, CTFPHC, GIN, MAGICapp, PubMed, EuropePMC, TRIP, and OpenAlex. Covers disease management, cardiology, oncology, diabetes, pharmacogenomics, and more. Use when users ask about clinical guidelines, treatment recommendations, standard of care, evidence-based medicine, or drug-gene dosing recommendations.

wu-yc
wu-yc
research
open
academic
950

drug-labels-search

Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu.

wu-yc
wu-yc
research
open
astronomy-physics
950

omero-integration

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

wu-yc
wu-yc
research
open
astronomy-physics
950

geopandas

Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-immune-repertoire-analysis

Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict epitope specificity. Integrate with single-cell data for clonotype-phenotype associations. Use for adaptive immune response profiling, cancer immunotherapy research, vaccine response assessment, autoimmune disease studies, or repertoire diversity analysis in immunology research.

wu-yc
wu-yc
research
open
bioinformatics
950

pysam

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

wu-yc
wu-yc
research
open
bioinformatics
950

pydeseq2

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

wu-yc
wu-yc
research
open
bioinformatics
950

cellxgene-census

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

wu-yc
wu-yc
research
open
bioinformatics
950

analyze-lab-video-cell-behavior

Automated cell behavior analysis from microscopy or XR lab recordings. Classifies cell motion phenotypes (migration, proliferation, apoptosis, division, quiescence), computes population-level quantitative metrics (growth rate, migration velocity, directionality index), and emits structured JSON for downstream reporting, plotting, or ELN integration.

wu-yc
wu-yc
research
open
bioinformatics
950

alphafold-database

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-protein-therapeutic-design

Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation. Use when asked to design protein binders, therapeutic proteins, or engineer protein function.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-target-research

Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug interactions, and literature. Features collision-aware searches, evidence grading (T1-T4), explicit Open Targets coverage, and mandatory completeness auditing. Use when users ask about drug targets, proteins, genes, or need target validation, druggability assessment, or comprehensive target profiling.

wu-yc
wu-yc
research
open
bioinformatics
950

torchdrug

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

wu-yc
wu-yc
research
open
bioinformatics
950

geo-database

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.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-multi-omics-integration

Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision medicine. Performs cross-omics correlation, multi-omics clustering (MOFA+, NMF), pathway-level integration, and sample matching. Coordinates ToolUniverse skills for expression data (RNA-seq), epigenomics (methylation, ChIP-seq), variants (SNVs, CNVs), protein interactions, and pathway enrichment. Use when analyzing multi-omics datasets, performing integrative analysis, discovering multi-omics biomarkers, studying disease mechanisms across molecular layers, or conducting systems biology research that requires coordinated analysis of transcriptome, genome, epigenome, proteome, and metabolome data.

wu-yc
wu-yc
research
open
bioinformatics
950

gwas-database

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-gwas-study-explorer

Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to compare study designs, effect sizes, ancestry diversity, and heterogeneity statistics. Use when comparing GWAS studies for a trait, performing meta-analysis of genetic loci, assessing replication across cohorts, or exploring the genetic architecture of complex diseases.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-gwas-snp-interpretation

Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar). Retrieves variant annotations, GWAS trait associations, fine-mapping evidence, locus-to-gene predictions, and clinical significance. Use when asked to interpret a SNP by rsID, find disease associations for a variant, assess clinical significance, or answer questions like "What diseases is rs429358 associated with?" or "Interpret rs7903146".

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-gwas-trait-to-gene

Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions). Identifies genetic risk factors, prioritizes causal genes via locus-to-gene scoring, and assesses druggability. Use when asked to find genes associated with a disease or trait, discover genetic risk factors, translate GWAS signals to gene targets, or answer questions like "What genes are associated with type 2 diabetes?"

wu-yc
wu-yc
research
open
bioinformatics
950

neuropixels-analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-expression-data-retrieval

Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-gene-enrichment

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis.

wu-yc
wu-yc
research
open
bioinformatics
950

tooluniverse-gwas-drug-discovery

Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, existing drug identification, safety profile evaluation, and clinical trial matching. Use when discovering drug targets from GWAS data, finding drug repurposing opportunities from genetic associations, or translating GWAS findings into therapeutic leads.

wu-yc
wu-yc
research
open
bioinformatics
950

string-database

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.

wu-yc
wu-yc
research
open
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