entrez

Brings bulk and pseudobulk transcriptomics to the tidyverse

Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.

😴 📂 Create and Query a Local Copy of GenBank in R

MCP SDK v2 server for PubMed and multi-source biomedical research, with resilient search, full text, citations, and tenant-safe deployment.

A Rust wrapper around the Entrez API. Helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.

Sentinel is an AI agent that retrieves PubMed publications using phi3.5 with phidata to generate and run a MeSH search on NCBI Entrez.

Extract figures and figure captions from PMC open access papers

Materials used for introductory classes using Julia for statistics, biomedical queries and plotting

Python scripts for searching Pubmed using Biopython and working with eponymous terms

Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.

Multi-agentic biomedical literature evidence extraction, curation, and summarization from PubMed/PMC in Open Knowledge Format (OKF) for downstream machine learning, feature selection, and agentic applications.

A VSM-dictionary that uses NCBI's E-utilities API to connect with the PubMed database

🦇🦠🌳Study on detection of Brno loanvirus in Southern Russia

Python class project in collab with @heloint and @AniValle. Using Entrez, Seq.io, regex, pandas

Parse HTTP response as stream, by chunks. Example for NCBI (PubMed) Entrez.

Genes for Project Cognoma

NCBI Entrez db web interface and api

Alembic is a comprehensive platform for fetching and analyzing biological and biomedical metadata. It provides a unified interface to access NCBI databases and extract named entities from biomedical text.

Sequencing data preprocessing