Backend & APIs · Bioinformatics

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.).

google-deepmind/science-skills

Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.

QING1105/ezST

Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice.

NVIDIA/skills

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

Query metadata and download data from the PRIDE Archive, EMBL-EBI's proteomics identifications database, via the PRIDE Archive REST API v3.

ClawBio/ClawBio

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

aipoch/medical-research-skills

Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads.

jaechang-hits/SciAgent-Skills

JASPAR 2024 TF binding profiles via REST API and pyJASPAR. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.

jaechang-hits/SciAgent-Skills

Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.

jaechang-hits/SciAgent-Skills

Query EBI QuickGO REST API for GO terms and protein annotations.

jaechang-hits/SciAgent-Skills

Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state).

jaechang-hits/SciAgent-Skills

Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants.

jaechang-hits/SciAgent-Skills

NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS.

jaechang-hits/SciAgent-Skills

KEGG REST API (academic only). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing.

jaechang-hits/SciAgent-Skills

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need…

aipoch/medical-research-skills

Query gene, sequence, and variant data via the Ensembl REST API

wentorai/research-plugins

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug…

jaechang-hits/SciAgent-Skills

Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.

jaechang-hits/SciAgent-Skills

Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping.

jaechang-hits/SciAgent-Skills

Query InterPro REST API for protein domain architecture, family classification, and member-DB integration.

jaechang-hits/SciAgent-Skills

Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.

jaechang-hits/SciAgent-Skills

Annotate and filter VCF variants with SnpEff and SnpSift. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download…

jaechang-hits/SciAgent-Skills

Selects, investigates, and compares AWS object, file, and block storage services, and answers cost, performance, configuration, security, and troubleshooting questions about storage services.

aws/agent-toolkit-for-aws

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way.

bioMate-AI/biomate-bioconductor-kb