Wanjun Gu
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About Me

I am a graduate student in the Biological and Medical Informatics PhD program at UCSF and a data scientist at Steps2walk.

I am interested in exploring the potential of scientific computing and machine learning in the fields of genetics, medical imaging, and epidemiology.

I am passionate about statistical programming and the open source initiative, therefore I love using R.

Skill Set

  • Programming Languages: R, Python, BASH, MATLAB, C++, Julia
  • Web Development: R Shiny, React, JavaScript, Node.js, HTML5, CSS
  • Project Management: Git, GitHub, Markdown
  • Design: Illustrator, Photoshop
  • Miscellaneous: ImageJ

Software

tKOI

The transcriptomic Knowledge-graph-driven Omics Integration for Human Pathway Analysis (tkoi) package provides an integrative framework that combines transcriptomic data with a human-specific biological knowledge graph. This enables network-aware enrichment, functional interpretation, and gene prioritization via personalized PageRank and ontology-aware annotation.

Documentation
pKOI

pKOI (Proteomic Knowledge-graph-driven Omics Integration) is a network-based enrichment analysis tool that integrates differential proteomics data with a heterogeneous biological knowledge graph. It uses a personalized PageRank algorithm to prioritize and annotate biologically relevant nodes (e.g., genes, diseases, pathways, cell types) connected to significant proteins.

Documentation
KDPS

KDPS (Kinship Decouple and Phenotype Selection) is an R package designed to resolve cryptic relatedness in genetic studies using a phenotype-aware approach. It retains subjects with relevant traits while pruning related individuals based on kinship or identity-by-descent (IBD) scores.

Documentation
ggmugs

A 'grammar of graphics' approach for visualizing summary statistics from multiple Genome-wide Association Studies (GWAS). It offers geneticists, bioinformaticians, and researchers a powerful yet flexible tool for illustrating complex genetic associations using data from various GWAS datasets. The visualizations can be extensively customized, facilitating detailed comparative analysis across different genetic studies.

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bolt4jr

bolt4jr: Interface for the 'Neo4j Bolt' Protocol. Querying, extracting, and processing large-scale network data from Neo4j databases using the 'Neo4j Bolt' protocol. This interface supports efficient data retrieval, batch processing for large datasets, and seamless conversion of query results into R data frames, making it ideal for bioinformatics, computational biology, and other graph-based applications.

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gptr

gptr: An R Interface with the ChatGPT API. A convenient interface with the OpenAI 'ChatGPT' API . 'gptr' allows you to interact with 'ChatGPT', a powerful language model, for various natural language processing tasks. The 'gptr' R package makes talking to 'ChatGPT' in R super easy. It helps researchers and data folks by simplifying the complicated stuff, like asking questions and getting answers. With 'gptr', you can use 'ChatGPT' in R without any hassle, making it simpler for everyone to do cool things with language!

view on CRAN