aipoch/medical-research-skills - Page 11

scrna-cell-type-annotator

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

Langue du texte source : anglais

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).

Langue du texte source : anglais

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.

Langue du texte source : anglais

sequence-alignment

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

smiles-de-salter

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

Langue du texte source : anglais

spatial-transcriptomics-mapper

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

Langue du texte source : anglais

statistical-analysis-advisor

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

Langue du texte source : anglais

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…

Langue du texte source : anglais

survival-curve-risk-table

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

Langue du texte source : anglais

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…

Langue du texte source : anglais

toxicity-structure-alert

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

Langue du texte source : anglais

upset-plot-converter

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

Langue du texte source : anglais

variant-pathogenicity-predictor

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

Langue du texte source : anglais

volcano-plot-labeler

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

western-blot-quantifier

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

Langue du texte source : anglais

acronym-unpacker

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

bio-ontology-mapper

Map unstructured biomedical text to standardized ontologies (SNOMED CT.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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…

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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…

Langue du texte source : anglais

comparison-table-gen

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

Langue du texte source : anglais

competitor-trial-monitor

Monitor competitor clinical trial progress and alert on market risks.

Langue du texte source : anglais

concept-explainer

Uses analogies to explain complex medical concepts in accessible terms.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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…

Langue du texte source : anglais