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

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

Extract figures and figure captions from PMC open access papers

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

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

Genes for Project Cognoma

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

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.

This is a Kaggle competition sponsored by Memorial Sloan Kettering Cancer Center. This competition is the first step in personalized medicine to determine oncogenicity of a tumor. Algorithm using sparse words to predict gene mutations effect on protein function.

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!

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

Sequencing data preprocessing

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.

Query entrez databases using R, returns document summaries as data frame. Wrapper function around esearch and esummary etools.