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.

:sleeping: :open_file_folder: 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.

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

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

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.

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

Genes for Project Cognoma

No description provided.

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

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.

Token-aware PubMed article fetcher with MeSH support and intelligent batching for LLM pipelines

This script iterates over an excel file with Genbank accession numbers. It creates individual fasta files with customized deflines for every valid accession number. It also creates a combined fasta file and .txt file with every valid accession number.

Sequencing data preprocessing

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

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

Modification of the Biopython Entrez module to be compatible with AWS Lambda.

🧬 Automated AI pipeline that monitors NCBI PubMed, generates bilingual (EN/TR) science blog posts using Google Gemini 1.5, and archives metadata in Supabase.

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.

Este é um repositório de um pipeline de dados, uma ferramenta automatizada e robusta projetada para efetuar a estração de sequências genéticas utilizando a API Entrez do GenBank. Este pipeline é o resultado de um esforço contínuo para facilitar o acesso e a manipulação de dados genéticos de importância global, com foco atual no vírus Chikungunya.

Course Work for Practical Bioinformatics Course BIO231, Assignments of BLAST,GenBANK search, NCBI ENTREZ API. Microarray Analysis

I'm passionate about Cloud and DevOps, and for the moment I'm posting some of my work and personal projects here to showcase that. If its useful for you, feel free to integrate or contribute!

Web scraping with Python