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

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.

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

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

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

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

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

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

Genes for Project Cognoma

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

EzMetaServer 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.

This Python script automates the process of retrieving first author affiliations for academic publications using the NCBI E-utilities API. It processes a CSV file containing DOIs (Digital Object Identifiers) and fetches the corresponding first author affiliations from PubMed.

A Python command-line tool to fetch research papers from PubMed and identify papers with authors affiliated with pharmaceutical or biotech companies.

Sequencing data preprocessing

Repository for BioPython class, belonging to the Undergraduate Program in Genomic Sciences, UNAM.