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Search NCBI , found 12 results

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ClinVar Variant Explorer

clinvar-database

K-Dense-AI/claude-scientific-skills

Query NCBI ClinVar for variant clinical significance, mixing gene/condition searches, API/FTP downloads, and VCF annotations to support genomic medicine interpretation workflows.

Phylogenetic Tree Toolkit

K-Dense-AI/claude-scientific-skills

A toolkit for phylogenetic tree manipulation, event detection, NCBI taxonomy integration, and publication-quality visualization, streamlining phylogenomics workflows and gene family analysis.

NCBI Gene Explorer

K-Dense-AI/claude-scientific-skills

Access NCBI Gene data via E-utilities or Datasets API to look up genes by symbol or ID, retrieve RefSeqs, GO terms, chromosomal locations, phenotypes, and run batch workflows for annotation pipelines.

GEO Data Retriever

K-Dense-AI/claude-scientific-skills

Connect to NCBI's GEO repository, search series/samples/platforms via Entrez queries, fetch profiles, and download raw/processed matrices using GEOparse for transcriptomics and expression analysis workflows.

PubMed Database Access

pubmed-database

K-Dense-AI/claude-scientific-skills

Direct REST/API access to PubMed for constructing complex Boolean or MeSH queries, filtering by publication attributes, and automating literature retrieval or citation management via NCBI’s E-utilities.

Biopython Bioinformatics Toolkit

K-Dense-AI/scientific-agent-skills

Comprehensive Python toolkit for molecular biology: sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access. Ideal for batch processing, custom bioinformatics pipelines, and BLAST automation.

ETE4 Phylogenetic Tree Toolkit

K-Dense-AI/scientific-agent-skills

Analyze, edit, compare, annotate and visualize phylogenetic or hierarchical trees with ETE 4. Supports Newick/Nexus I/O, rooting and pruning, Robinson-Foulds topology comparison, gene-tree evolutionary events, NCBI/GTDB taxonomy queries and SmartView rendering.

Biomedical Literature Search Using PubMed API

pubmed-database

affaan-m/everything-claude-code

This guide provides a comprehensive workflow for searching and retrieving biomedical literature from PubMed and NCBI. It covers advanced query construction using MeSH terms and specific field tags, advanced filtering (date, publication type), and a repeatable programmatic workflow using NCBI E-utilities (esearch, efetch). Essential for researchers conducting systematic reviews and literature monitoring.

Biomedical Literature Search Using PubMed API

pubmed-database

This guide provides a comprehensive workflow for searching and retrieving biomedical literature from PubMed and NCBI. It covers advanced query construction using MeSH terms and specific field tags, advanced filtering (date, publication type), and a repeatable programmatic workflow using NCBI E-utilities (esearch, efetch). Essential for researchers conducting systematic reviews and literature monitoring.

Biopython: Computational Biology Toolkit

sickn33/antigravity-awesome-skills

Biopython is a comprehensive Python library designed for computational molecular biology. It provides robust tools for handling biological sequences (DNA, RNA, Protein), structural analysis (PDB), sequence alignment, phylogenetic tree construction, and interfacing with major public databases like NCBI (Entrez). Ideal for researchers performing advanced bioinformatics tasks.

Mining PubMed Literature with NCBI E-utilities

mining-pubmed-literature

maziyarpanahi/openmed

This skill programmatically searches and fetches biomedical literature from PubMed and PMC using NCBI E-utilities (ESearch, EFetch, ESummary). It allows users to gather large corpora of abstracts, full texts, and metadata related to specific conditions, drugs, or genes. Ideal for building evidence bases, performing biomedical Named Entity Recognition (NER), or summarizing scientific findings.

PubMed Literature Search Workflow

scientific-db-pubmed-database

Search PubMed biomedical literature via NCBI E-utilities: build MeSH and field-tag queries, filter by publication type and date, retrieve PMIDs, abstracts, and citations for systematic reviews and literature monitoring.

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