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

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.

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

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.

Extract figures and figure captions from PMC open access papers

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.

🦇🦠🌳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.

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.

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!

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

MCP server for PubMed/NCBI literature search with PICO analysis, search strategies, and session management

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

Web scraping with Python

fetche sequences in ncbi