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NCBI agent skills for Claude Code, Codex and other agents.
- skills
- 98
- Type
- Other
- Website
- ncbi.nlm.nih.gov
NCBI skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. | google-deepmind/ | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 | 22 days ago |
| 2 | 2.Jj Flow jujutsu (jj) command cheatsheet for this colocated jj+git Bioconductor repo. | seandavi/ | 118 | — | ~981 | Automated safety check: Pass | Unknown | 1 mo ago |
| 3 | Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis. | aiming-lab/ | 15k | — | ~810 | Automated safety check: Pass | MIT | 1 mo ago |
| 4 | Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. | GPTomics/ | 1.2k | 3 repos | ~2.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | 穗织世界观、神话与诅咒、身边人物、API速查表——常陆茉子的背景知识库，自动加载. An agent skill from liebaojun/MakoCode. | liebaojun/ | 155 | — | ~692 | Automated safety check: Pass | Unknown | 1 mo ago |
| 6 | Searches PubMed directly through its E-utilities REST API, with guidance on Boolean and MeSH query syntax, batch retrieval and citation data. | davila7/ | 32k | 15 repos | ~3.9k | Automated safety check: Pass | MIT | today |
| 7 | Guides your agent through building, editing, comparing and drawing phylogenetic trees with the ETE Python toolkit, including orthology calls and NCBI taxonomy lookups. | davila7/ | 32k | 12 repos | ~4.5k | Automated safety check: Notes | MIT | today |
| 8 | Query NCBI Gene via E-utilities/Datasets API. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 10 repos | ~1.6k | Automated safety check: Pass | MIT | today |
| 9 | Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 13 repos | ~3.4k | Automated safety check: Pass | MIT | today |
| 10 | Query NCBI ClinVar for variant clinical significance. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 11 repos | ~3.3k | Automated safety check: Pass | MIT | today |
| 11 | Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. | wu-yc/ | 1.1k | 2 repos | ~4k | Automated safety check: Pass | No licence | 6 mo ago |
| 12 | Search PubMed for scientific literature, including published clinical trials. | google-deepmind/ | 3.2k | 2 repos | ~2.1k | Automated safety check: Notes | Apache-2.0 | 22 days ago |
| 13 | Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools. | ClawBio/ | 1.2k | 1 repo | ~2.8k | Automated safety check: Pass | MIT | yesterday |
| 14 | Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. | google-deepmind/ | 3.2k | 1 repo | ~2.3k | Automated safety check: Notes | Apache-2.0 | 22 days ago |
| 15 | 15.Geo Database Access NCBI GEO for gene expression/genomics data. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 11 repos | ~6.1k | Automated safety check: Pass | MIT | today |
| 16 | Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal… | aipoch/ | 2k | — | ~1.7k | Automated safety check: Pass | MIT | 20 days ago |
| 17 | Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 370 | 1 repo | ~4.4k | Automated safety check: Pass | CC-BY-4.0 | 8 days ago |
| 18 | Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring. | affaan-m/ | 274k | 1 repo | ~1.2k | Automated safety check: Pass | MIT | 2 days ago |
| 19 | 19.Etetoolkit Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. | K-Dense-AI/ | 48k | 1 repo | ~3.3k | Automated safety check: Notes | GPL-3.0-or-later | 2 days ago |
| 20 | Load when converting gene identifiers between Ensembl, Entrez, and HGNC symbol in a bulk RNA-seq count matrix. | TianGzlab/ | 161 | — | ~1k | Automated safety check: Pass | MIT | 2 mo ago |
| 21 | Searches and fetches PubMed and PMC via NCBI E-utilities (ESearch then EFetch/ESummary) to gather biomedical evidence and build text corpora. | maziyarpanahi/ | 5.5k | — | ~1.7k | Automated safety check: Pass | Apache-2.0 | yesterday |
| 22 | 22.Biopython Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). | K-Dense-AI/ | 48k | 1 repo | ~4.3k | Automated safety check: Notes | MIT | 2 days ago |
| 23 | 23.Biopython Computational molecular biology library (sequence I/O, alignment, phylogenetics). | lamm-mit/ | 244 | — | ~3.9k | Automated safety check: Pass | Apache-2.0 | 1 mo ago |
| 24 | Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. | FreedomIntelligence/ | 3.1k | 2 repos | ~2.5k | Automated safety check: Notes | No licence | 2 mo ago |
| 25 | Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. | wu-yc/ | 1.1k | 2 repos | ~4.2k | Automated safety check: Pass | No licence | 6 mo ago |
| 26 | Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. | wu-yc/ | 1.1k | 2 repos | ~2.7k | Automated safety check: Pass | No licence | 6 mo ago |
| 27 | 27.Search Lit A skill your agent uses when finding papers or building a reference list. | Aperivue/ | 329 | — | ~4.7k | Automated safety check: Pass | MIT | 2 days ago |
| 28 | 生物医学文献、MeSH クエリ、PMID 検索、引用取得、および API を利用した文献モニタリングのための PubMed および NCBI E-utilities の直接検索ワークフロー。 | affaan-m/ | 274k | — | ~908 | Automated safety check: Pass | MIT | 2 days ago |
| 29 | In recent years a wealth of biological data has become available in public data repositories. | bioMate-AI/ | 804 | — | ~4.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 30 | Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 31 | Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. | GPTomics/ | 1.2k | 2 repos | ~3.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 32 | Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 33 | 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/ | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 34 | Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 35 | Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). | GPTomics/ | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 36 | 36.Bio Geo Data Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. | GPTomics/ | 1.2k | 2 repos | ~4.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 37 | Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. | GPTomics/ | 1.2k | 2 repos | ~4.1k | Automated safety check: Notes | MIT | 1 mo ago |
| 38 | Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assemblysummary.txt scraping and many EFetch workflows). | GPTomics/ | 1.2k | 2 repos | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 39 | 39.Bio Sra Data Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. | GPTomics/ | 1.2k | 2 repos | ~4k | Automated safety check: Pass | MIT | 1 mo ago |
| 40 | Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 41 | Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 42 | Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 43 | Search PubMed for scientific literature. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~751 | Automated safety check: Pass | No licence | 2 mo ago |
| 44 | Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. | GPTomics/ | 1.2k | 2 repos | ~5.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 45 | Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB)… | GPTomics/ | 1.2k | 2 repos | ~8.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 46 | Search PubMed, preserve complete abstracts and sections, and produce research briefings with abstract openings or optional OpenAI/Ollama summaries. | ClawBio/ | 1.2k | — | ~3.3k | Automated safety check: Pass | MIT | yesterday |
| 47 | NCBI Gene via E-utilities: curated records across 1M+ taxa. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 370 | 1 repo | ~4.4k | Automated safety check: Pass | CC0-1.0 | 8 days ago |
| 48 | 48.Sragent Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. | aiskillstore/ | 430 | 2 repos | ~3.5k | Automated safety check: Pass | No licence | today |
Questions, answered from the data.
What is the best NCBI skill?
Dbsnp Database from google-deepmind/science-skills ranks first of the 98 NCBI skills listed here, with the highest score: its repository has 3.2k GitHub stars, 2 other GitHub owners carry a copy, its SKILL.md loads about 3.4k tokens and it has informational notes only in the automated safety check. Next come Jj Flow and Biopython Bioinformatics.
Is there an official NCBI skill?
None yet. All 98 NCBI skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.