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

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

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

Genes for Project Cognoma

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.

Web scraping with Python

fetche sequences in ncbi

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

Sequencing data preprocessing

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

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.