Results for “genetic-data”

Guides DPIA for health and medical data processing covering Art. 9(2)(h)-(j) exemptions, HIPAA crosswalk for transatlantic operations, clinical trial data protection under EU CTR 536/2014, and genetic data specifics under Art. 9(1). Activate for healthcare systems, clinical research, health apps, or medical device data. Keywords: health data, DPIA, Art. 9, clinical trial, genetic data, HIPAA, medical records, special category.

CPRA §1798.121 sensitive personal information restrictions and compliance. Covers all 9 sensitive PI categories including SSN, precise geolocation, racial/ethnic origin, biometric, genetic, health, and sex life data. Right to limit use/disclosure, permitted purposes, and implementation.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Create, read, manipulate, and store annotated data matrices using the AnnData Python package, designed for single-cell genomics and general-purpose annotated data workflows.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Quickly query genomic reference databases for Ensembl IDs, gene metadata, sequences, BLAST searches, and enrichment analysis using the gget CLI or Python package.

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.

Emu: Generative Pretraining in Multimodality

Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

Kit de ferramentas CLI/Python para consultas rápidas de bioinformática. Preferido para buscas BLAST rápidas. Acesso a 20+ bancos de dados: informações de genes (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, downloads de genoma. Para BLAST avançado/processamento em lote, use biopython. Para integração multi-banco de dados, use bioservices.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Manages annotated data matrices for single-cell genomics, covering creation, I/O, concatenation, and manipulation of AnnData objects in h5ad and zarr formats.

Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.

Queries the ClinPGx REST API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels, generating markdown reports with CSV tables.

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Document datasets, variables, sources, and merge keys for replication

Casting personas: rapid generation from diverse inputs, registry-based persistence and lifecycle, data-driven evolution, inter-agent sync. Not for UI walkthroughs (Echo) or user research (Field).

Builds a scheduled, AI-powered data collection agent that scrapes public sources, enriches results with Gemini Flash, and stores them in Notion, Sheets, or Supabase.

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

Expert en biotechnologies avancées (bioinformatics, genomics, CRISPR, drug discovery, DZ research)

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.

Analyzes raw genomic data (FASTQ/VCF) to generate non-medical wellness, longevity, and pharmacogenomic optimization protocols while keeping DNA processing local and private.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.

Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.