Skills and MCP tagged “genomics”

start official anthropics skill Checks connected MCP servers and surveys bio-research tools. Helps researchers get oriented with the plugin before starting a project. Claude Code CX Codex Cursor +1 4,900installs scvi-tools official anthropics skill A skill providing deep learning workflows for single-cell genomics with scvi-tools. It guides model selection, batch correction, and AnnData processing pipelines. Claude Code CX Codex Cursor +1 2,400installs database-lookup K-Dense-AI skill Queries 80 documented public database APIs with explicit filters, pagination, and provenance. It is useful when scientific or financial facts require reproducible citations. Claude Code CX Codex Cursor +1 2,100installs dnanexus-integration K-Dense-AI skill Automates genomics workloads on DNAnexus using dx CLI, dxpy, and dxCompiler. Handy when building dxapp.json applets or importing Nextflow and WDL pipelines. Claude Code CX Codex Cursor +1 1,900installs polars-bio K-Dense-AI skill Genomic interval arithmetic on Polars DataFrames, plus readers and writers for formats from BED to CRAM. Built for coordinate-aware joins in a Python pipeline. Claude Code CX Codex Cursor +1 1,900installs gtars K-Dense-AI skill Skill for genomic interval analysis, overlaps, consensus and coverage via Python, Rust and CLI. Requires Python 3.10+ and gtars 0.10.0; local tools run offline. Claude Code CX Codex Cursor +1 1,900installs geniml K-Dense-AI skill Checks BED and genomic-universe contracts, then plans Region2Vec and scEmbed runs. Use it before local genomic-interval analysis. Claude Code CX Codex Cursor +1 1,900installs depmap K-Dense-AI skill A skill for discovering and analyzing Cancer Dependency Map data. Helps examine CRISPR Chronos gene effects, co-essentiality, and PRISM compound responses. Claude Code CX Codex Cursor +1 1,900installs pysam K-Dense-AI skill Guides agents through Python and HTSlib workflows for genomic files like BAM, CRAM, and VCF. Useful when extracting alignments, filtering reads, and computing coverage. Claude Code CX Codex Cursor +1 1,900installs cellxgene-census K-Dense-AI skill A skill for programmatic access to CZ CELLxGENE Census, a vast catalog of standardized single-cell transcriptomics data. Query metadata, gene expression, and embeddings without downloading entire datasets. Claude Code CX Codex Cursor +1 1,900installs gget K-Dense-AI skill Bioinformatics skill providing unified access to over 20 genomic databases via CLI and Python. Useful for gene lookups, alignments, and protein structure downloads. Claude Code CX Codex Cursor +1 1,900installs anndata K-Dense-AI skill Skill to create, read, and transform annotated data matrices in h5ad and Zarr formats. Integrates with the scverse ecosystem for transcriptomics and other metadata-rich data analysis. Claude Code CX Codex Cursor +1 1,900installs scikit-bio K-Dense-AI skill Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. Helpful for microbiome workflows and ecology data. Claude Code CX Codex Cursor +1 1,900installs hugging-science K-Dense-AI skill A skill to find and evaluate scientific datasets, models, and interactive demos via the Hugging Science catalog. Use it when you need an ML resource for biology, chemistry, genomics, materials science, climate, or physics. Claude Code CX Codex Cursor +1 1,800installs pacsomatic K-Dense-AI skill Prepares a matched tumor-normal run of nf-core/pacsomatic on PacBio HiFi data: builds the samplesheet, writes launch artifacts, submits the Nextflow driver to a scheduler. Claude Code CX Codex Cursor +1 1,400installs onekgpd K-Dense-AI skill Queries the 1000 Genomes Project cohort at the participant level. It identifies variant carriers across 3,202 individuals and calculates relatedness. Claude Code CX Codex Cursor +1 1,100installs genomic-coordinates K-Dense-AI skill Converts genomic coordinates between BED, VCF, and GTF formats, and normalises variant representations. Useful when reconciling coordinate systems, indels, and assembly contigs. Claude Code CX Codex Cursor +1 939installs ukb-topmed-phewas-skill official OpenAI skill Fetch a compact UKB-TOPMed PheWAS summary for one variant. Useful when the input arrives as an rsID or GRCh37/GRCh38 coordinates. CX Codex GP ChatGPT 13installs gtex-eqtl-skill official OpenAI skill This skill fetches GTEx single-tissue eQTL associations for one variant and turns rsID, GRCh37, or GRCh38 input into a GRCh38 query. It returns JSON. CX Codex GP ChatGPT 13installs eva-skill official OpenAI skill Sends compact queries to the European Variation Archive and returns concise summaries for species metadata or targeted variants. CX Codex GP ChatGPT 13installs encode-skill official OpenAI skill Runs compact ENCODE REST API queries for object lookups, catalog searches, and metadata summaries. Helpful for genomic data workflows. CX Codex GP ChatGPT 13installs