Shortcut functions to boost daily bioinformatic work

Data intensive science for everyone.

Scripts for de novo genome assembly

A proof of concept of RNAseq pipeline

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

An open-source toolkit for large-scale genomic analysis

🌿: ABM & GIS for philological, archaeological, and anthropological data.

CUT&RUN and CUT&Tag data processing and analysis

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Projects on COVID-19 topic of genomic sequencing - mostly DataViz

Here you'll find information about my background, expertise, and professional interests. As a physician and bioinformatic programmer, I'm passionate about leveraging my diverse skill set to make meaningful contributions to healthcare, research, and technology.

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research

Gene set variation analysis

This repository contains cancer data analysis from TCGA

Official code repository for GATK versions 4 and up

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted sequence properties and eliminates the need to manually extract and select features from phage sequences

Phage-host interaction prediction tool that incorporates protein structure information in representing receptor-binding proteins (RBPs). It improves performance especially for phages with RBPs that have low sequence similarity to those of known phages

Integrated Pipeline Reports (IPR) API, the reporting API as part of the PORI platform

Comparative Genomics Toolkit 3