Research & Science · Ensembl · By GPTomics

Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables.

GPTomics/bioSkills

Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species…

GPTomics/bioSkills

Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways.

GPTomics/bioSkills

Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chaining ambient-RNA removal, doublet detection, MAD-adaptive QC, normalization…

GPTomics/bioSkills

Annotates VCF variants with functional consequences, population frequencies, and pathogenicity scores using bcftools annotate/csq, Ensembl VEP, SnpEff, and ANNOVAR.

GPTomics/bioSkills