NCBI · For researchers

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

Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-reviewed, reaction-level pathways using ReactomePA's enrichPathway (ORA) and…

GPTomics/bioSkills

Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways.

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

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

Retrieves comprehensive gene information including PubMed publication counts, NCBI summaries, and Ensembl transcript data.

aipoch/medical-research-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

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF.

FreedomIntelligence/OpenClaw-Medical-Skills

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases.

FreedomIntelligence/OpenClaw-Medical-Skills

Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees.

jaechang-hits/SciAgent-Skills

Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic…

jaechang-hits/SciAgent-Skills

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

jaechang-hits/SciAgent-Skills

KEGG REST API (academic only). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Generates academic reviews for molecules in diseases using PubMed research.

aipoch/medical-research-skills

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

aipoch/medical-research-skills

Query gene, variant, and drug annotations via BioThings APIs

wentorai/research-plugins

Access genomes, genes, and taxonomy data via NCBI Datasets v2 API

wentorai/research-plugins

Search biomedical literature and retrieve records via PubMed E-utilities

wentorai/research-plugins

Retrieve gene information from NCBI Gene database by gene IDs to obtain genomic details, function, and expression data.

InternScience/scp

Query dbSNP + NCBI Gene to get variant genomic position (chromosome, coordinates, ref/alt alleles, mutation type) and associated gene coordinates.

InternScience/scp

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline.

jaechang-hits/SciAgent-Skills

Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.

jaechang-hits/SciAgent-Skills

ENA REST API for sequences, reads, assemblies, and annotations.

jaechang-hits/SciAgent-Skills

Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline.

jaechang-hits/SciAgent-Skills

Search PubMed for scientific literature and retrieve abstracts

lamm-mit/scienceclaw

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

InternScience/scp

cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set.

bioMate-AI/biomate-bioconductor-kb

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases.

bioMate-AI/biomate-bioconductor-kb

Search NCBI BLAST for sequence homology and find similar sequences in biological databases

lamm-mit/scienceclaw

Analyze biological sequences using Biopython - translate, align, parse FASTA/GenBank

lamm-mit/scienceclaw

ToolUniverse workflow — Sequence Retrieval. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw