aipoch/medical-research-skills - Page 11

scrna-cell-type-annotator

Auto-annotate cell clusters from single-cell RNA data using marker genes.

scvi-tools

Deep generative models for single-cell omics; use when you need probabilistic batch correction (scVI), transfer learning, uncertainty-aware differential expression, or multimodal integration (totalVI/MultiVI).

seaborn

Statistical visualization library integrated with pandas; use it when you need fast EDA of distributions, relationships, and categorical comparisons (e.g., box/violin/pair plots and heatmaps) with strong default aesthetics on top of matplotlib.

sequence-alignment

A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.

singlecell-portal

Programmatically query public single-cell study metadata from the Broad Institute Single Cell Portal REST API when you need to search and filter datasets by organism, tissue, disease, or cell type without an API key.

smiles-de-salter

Analyze data with `smiles-de-salter` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

spatial-transcriptomics-mapper

Map spatial transcriptomics data from 10x Genomics Visium/Xenium onto.

statistical-analysis-advisor

Recommends appropriate statistical methods (T-test vs ANOVA, etc.) based.

study-design-scale-selector

Determines the appropriate Risk of Bias assessment scale for a medical study based on its design (RCT, Cohort, etc.), using PubMed metadata lookup or text analysis. Use when the user wants to know which quality assessment tool to use for a specific paper…

survival-curve-risk-table

Analyze data with `survival-curve-risk-table` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

torchdrug-english

PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, and…

toxicity-structure-alert

Analyze data with `toxicity-structure-alert` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

upset-plot-converter

Convert complex Venn diagrams with more than 4 sets to clearer Upset.

variant-pathogenicity-predictor

Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity.

volcano-plot-labeler

Analyze data with `volcano-plot-labeler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

volcano-plot-script

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.

western-blot-quantifier

Automatically identify Western Blot gel bands, perform densitometric analysis, and calculate normalized values relative to loading controls.

acronym-unpacker

Intelligent medical abbreviation disambiguation tool that resolves ambiguous acronyms using clinical context, specialty-specific knowledge, and document-level semantic analysis.

alphafold-db

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

arboreto

Infer gene regulatory networks (GRNs) from gene expression matrices using GRNBoost2 or GENIE3; use when analyzing bulk or single-cell RNA-seq to identify TF→target regulatory relationships.

arxiv-database

Search and retrieve scientific preprints from arXiv; use it when you need to find papers by keyword/author/category, fetch metadata (abstract, DOI, PDF URL), or download PDFs for offline reading.

bio-ontology-mapper

Map unstructured biomedical text to standardized ontologies (SNOMED CT.

biogrid-orcs

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.

biopython-entrez

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

biorxiv-database

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

blockbuster-therapy-predictor

Comprehensive analytics tool for forecasting breakthrough therapeutic technologies by integrating multi-dimensional data sources including clinical development pipelines, intellectual property landscapes, and capital mar.

brenda-database

Programmatic access to the BRENDA enzyme database via the SOAP API; use when you need kinetic constants (Km, kcat, Vmax), reaction equations, enzyme properties (pH/temperature optima, stability), or enzyme discovery by EC/substrate/product.

cellosaurus-api

Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.

cellxgene-census

Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.

chea-api

Access ChEA3 and Harmonizome ChEA data for transcription factor enrichment analysis and metadata retrieval. Use when the user needs to perform ChEA3 enrichment analysis on a gene set, get metadata about the ChEA dataset, or retrieve information about a…

chembl-database

Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure (SMILES), or retrieve drug mechanism information.

clinical-study-info-extractor

Batch extracts and verifies structured information (PMID, title, abstract, methodology, results, etc.) from clinical research literature using PMIDs. Use when the user wants to extract details from specific PMIDs.

clinicaltrials-db

Query the ClinicalTrials.gov API v2 to search for clinical trials, retrieve detailed study protocols, and analyze recruitment status; use when you need to find trials by condition/drug, export results, or verify study details by NCT ID.

clinpgx-database

Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.

clinvar-database

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF…

comparison-table-gen

Auto-generates comparison tables for concepts, drugs, or study results.

competitor-trial-monitor

Monitor competitor clinical trial progress and alert on market risks.

concept-explainer

Uses analogies to explain complex medical concepts in accessible terms.

cosmic-database

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

cross-disciplinary-bridge-finder

Use when identifying collaboration opportunities across fields, finding experts in complementary disciplines, translating methodologies between scientific domains, or building interdisciplinary research teams. Identifies synergies between scientific…