NCBI

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/science-skills

jujutsu (jj) command cheatsheet for this colocated jj+git Bioconductor repo.

seandavi/GEOquery

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

aiming-lab/AutoResearchClaw

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.

GPTomics/bioSkills

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/MakoCode

Searches PubMed directly through its E-utilities REST API, with guidance on Boolean and MeSH query syntax, batch retrieval and citation data.

davila7/claude-code-templates

Guides your agent through building, editing, comparing and drawing phylogenetic trees with the ETE Python toolkit, including orthology calls and NCBI taxonomy lookups.

davila7/claude-code-templates

Query NCBI Gene via E-utilities/Datasets API. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.

wu-yc/LabClaw

Query NCBI ClinVar for variant clinical significance. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Search PubMed for scientific literature, including published clinical trials.

google-deepmind/science-skills

Retrieve protein and nucleotide sequences from NCBI databases using E-utilities.

google-deepmind/science-skills

Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

ClawBio/ClawBio

Access NCBI GEO for gene expression/genomics data. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

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/medical-research-skills

Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.

affaan-m/ECC

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4.

K-Dense-AI/scientific-agent-skills

Searches and fetches PubMed and PMC via NCBI E-utilities (ESearch then EFetch/ESummary) to gather biomedical evidence and build text corpora.

maziyarpanahi/openmed

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

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).

K-Dense-AI/scientific-agent-skills

Computational molecular biology library (sequence I/O, alignment, phylogenetics).

lamm-mit/scienceclaw

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization.

FreedomIntelligence/OpenClaw-Medical-Skills

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

wu-yc/LabClaw

Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.

wu-yc/LabClaw

A skill your agent uses when finding papers or building a reference list.

Aperivue/medsci-skills

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/ECC

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

bioMate-AI/biomate-bioconductor-kb

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

GPTomics/bioSkills

Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables.

GPTomics/bioSkills

Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW.

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

Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary).

GPTomics/bioSkills

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).

GPTomics/bioSkills

Build local BLAST databases and run searches using NCBI BLAST+ command-line tools.

GPTomics/bioSkills

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/bioSkills

Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror.

GPTomics/bioSkills

Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.

GPTomics/bioSkills

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO.

FreedomIntelligence/OpenClaw-Medical-Skills

Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD.

FreedomIntelligence/OpenClaw-Medical-Skills

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO.

FreedomIntelligence/OpenClaw-Medical-Skills

Search PubMed for scientific literature. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG.

FreedomIntelligence/OpenClaw-Medical-Skills

Reactome pathway enrichment using ReactomePA package. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics.

FreedomIntelligence/OpenClaw-Medical-Skills

Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture.

GPTomics/bioSkills

Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB)…

GPTomics/bioSkills