Ensembl · Bioinformatics

Workflow for fixing or changing RNAlysis code that talks to an EXTERNAL WEB SERVICE — UniProt, Ensembl, PANTHER, PhylomeDB, OrthoInspector, KEGG, or GO.

GuyTeichman/RNAlysis

Query Ensembl genome database REST API for 250+ species. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and…

maziyarpanahi/openmed

CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP).

google-deepmind/science-skills

gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.

affaan-m/ECC

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.

TianGzlab/OmicsClaw

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

wu-yc/LabClaw

Production-ready RNA-seq differential expression analysis using PyDESeq2.

wu-yc/LabClaw

In recent years a wealth of biological data has become available in public data repositories.

bioMate-AI/biomate-bioconductor-kb

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

Production-ready genomics and epigenomics data processing for BixBench questions.

wu-yc/LabClaw

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

Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or…

aipoch/medical-research-skills

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

Unified CLI/Python interface to 20+ genomic databases. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

NCBI Gene via E-utilities: curated records across 1M+ taxa. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

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

GPTomics/bioSkills

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

jaechang-hits/SciAgent-Skills

Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.

jaechang-hits/SciAgent-Skills

Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI.

jaechang-hits/SciAgent-Skills

Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations.

jaechang-hits/SciAgent-Skills

Ensembl REST API for gene/transcript/variant annotations in 300+ species.

jaechang-hits/SciAgent-Skills

Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations.

jaechang-hits/SciAgent-Skills

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

wentorai/research-plugins

Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.

InternScience/scp

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

jaechang-hits/SciAgent-Skills

24 biomedical research skills. An agent skill from wentorai/research-plugins.

wentorai/research-plugins

Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers.

bioMate-AI/biomate-bioconductor-kb

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits.

bioMate-AI/biomate-bioconductor-kb