Backend & APIs · By GPTomics

Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic.

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

Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs.

GPTomics/bioSkills

Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes.

GPTomics/bioSkills

Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML.

GPTomics/bioSkills

Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP).

GPTomics/bioSkills

Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine selection, cache-vs-freeze semantics, native cross-references, parameters, and…

GPTomics/bioSkills

Creates reproducible R Markdown analysis reports (HTML, PDF, Word) with knitr, covering the render pipeline, the interactive-vs-knit session trap, cache invalidation, bookdown cross-references…

GPTomics/bioSkills

Tests gene lists, ranked vectors, and fold-change vectors against KEGG pathways and modules with clusterProfiler enrichKEGG/enrichMKEGG (ORA), gseKEGG (GSEA), and SPIA/graphite (signed-topology…

GPTomics/bioSkills