Name: Stephen "Christian" Kocsis
Type: User
Company: Mayo Clinic
Bio: Research technologist at Mayo Clinic, FL in Dr. Fairweather's Cardio-Immunology laboratory. Bioinformatics master's student at Johns Hopkins university.
Location: Jacksonville, FL
Blog: stephenkocsis.com
Stephen "Christian" Kocsis's Projects
This repo contains code for a nextflow pipeline to run a blast on biological sequences.
Integrate multiomic datasets using autoencoder-based feature extraction and perform GSEApy enrichr functional enrichment analysis on top features.
Nextflow pipelines for various bioinformatics, machine learning, and statistical analyses.
Easy to use RNA-sequencing data normalization tool built in C++ for use in Python. Can handle many popular normalization techniques.
Conduct a mass literature review using Python by inputting a key word or phrase of interest. This Python script can be used to query the PubMed database using Biopython. Input user email, how many papers you would like to be returned per query, and what date range you would like to have papers returned from.
This tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE and plotting using Pathview.
This is a tutorial of the weighted gene correlation network analysis (WGCNA) package from Dept. of Human Genetics, UC Los Angeles.