NCBI · Bioinformatics

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

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

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

davila7/claude-code-templates

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

davila7/claude-code-templates

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

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

K-Dense-AI/scientific-agent-skills

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

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

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

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

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

FreedomIntelligence/OpenClaw-Medical-Skills

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

Query metadata and download data from the NCBI Gene Expression Omnibus (GEO).

ClawBio/ClawBio

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…

aipoch/medical-research-skills

Search for gene expression DataSets and Profiles in the NCBI GEO database.

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

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO.

GPTomics/bioSkills

Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC…

GPTomics/bioSkills

Checks whether a PCR primer PAIR amplifies only the intended target genome-wide, using pair-aware in-silico PCR (MFEprimer-3.0, UCSC isPcr, NCBI Primer-BLAST) plus a primer3-py 3'-end-stability…

GPTomics/bioSkills

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access.

GPTomics/bioSkills

Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction.

GPTomics/bioSkills

Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding.

GPTomics/bioSkills

NCBI GEO access via GEOparse and E-utilities. 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

Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene).

jaechang-hits/SciAgent-Skills

Primary retained Python toolkit for molecular biology sequence work.

foryourhealth111-pixel/Vibe-Skills

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX…

GPTomics/bioSkills

Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit.

aiskillstore/marketplace

A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

aipoch/medical-research-skills

Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence…

aipoch/medical-research-skills