Results for “variant-query”

Store, query, and export genomic variant data (VCF/BCF) using TileDB's sparse array technology for scalable population genomics workflows.

Deploys Weaviate vector database with hybrid search, modules, and GraphQL API.

Guides selection of Qdrant search strategies including hybrid search, reranking, relevance feedback, MMR, and discovery APIs to improve retrieval quality.

Guides embedding model migration in Qdrant without downtime, covering alias swap, side-by-side, and hybrid search strategies.

Builds production RAG and semantic search systems with Qdrant, covering collection setup, vector indexing, filtered and hybrid search, and integration with LangChain and LlamaIndex.

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants, returning variants, carriers, and relatedness with allele frequencies and annotations.

Queries 9 genomic databases in parallel for a given rsID, returning unified GWAS, PheWAS, eQTL, and fine-mapping reports.

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.