cafferychen777 / microbiomestat-turtorial-professional-version

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

📊 Statistics PhD Student | 🧬 Multi-Omics Analyst | 🖥 R Package Developer

Hello! I'm Caffery Yang👋

I am thrilled to be joining the Statistics PhD program at Texas A&M University in Fall 2024. As a recent graduate from Southern Medical University, where I majored in Biostatistics and achieved a 3.95/4.00 GPA (top 2% of my class), I am currently visiting Jian Yang's Lab at Westlake University to further enrich my research experience before starting my doctoral studies.

🎖 Achievements

• Received the National Scholarship from the Ministry of Education of China.
• Secured First Prize in the National College Student Mathematics Competition.
• Honored with Meritorious Winner (M Award) in the Mathematical Contest in Modeling (MCM) in the USA.

🧪 Research Interests

Under the guidance of Prof. Jun Chen at Mayo Clinic and Prof. Liangliang Zhang at Case Western Reserve University, my research primarily revolves around microbiome data analysis.

• Developed the MicrobiomeStat R package, writing over 17,000 lines of R code. Comprehensive documentation is available on the package wiki, which contains in-depth guidance and tutorials exceeding 20,000 words. Additionally, an interactive MicrobiomeStat Shiny application has been created to provide a user-friendly platform for longitudinal statistical analysis and visualization of microbiome data.
• Pioneered the MicrobiomeGallery collaborative platform.
• Independently developed the ggpicrust2 R package, which amassed 85 stars on GitHub and over 11,000 downloads on CRAN.

My future vision embraces a multi-omics perspective, synthesizing insights from genomics, proteomics, transcriptomics, and more.

📚 Publications

• Sole first author on a paper accepted by Bioinformatics.
• Preparing to submit another paper as sole first author to Microbiome.

🤝 Collaboration

I am extremely open to collaborations. If you have any projects related to microbiomics or multi-omics and think we could work together, please don't hesitate to reach out. In addition to being open to new projects, I am particularly enthusiastic about assisting others with their microbiome/multi-omics data analysis. I'm also keen on collaborating with researchers and authors who have utilized my pipelines, such as ggpicrust2 or MicrobiomeStat, in their work. If you are considering or have already used these tools in your paper, I would be thrilled to explore the possibility of co-authorship. Whether it's contributing to data analysis, interpretation, or manuscript preparation, I am ready to bring my expertise to your research. Let's connect and see how we can advance the field of microbiomics together!

🛠 Projects

1. Application of LLM in Microbiome Taxonomy

Claude's innovative approach using the entire NCBI database with the LLM offers direct taxonomic insights from FASTQ sequences. A potential game-changer when compared with traditional methods.

2. Performance of Microbiome DA Methods in Other Omics

Exploring how microbiome DA methods, known for processing the compositional nature of microbiome data, perform on other omics.

3. Generative AI in Microbiome Data Analysis and Accuracy Assessment

Assessing the LLM model's capability as a microbiome data analysis expert against real-world experts.

4. PI_find

A tool designed to assist graduate school aspirants in discovering PI names from specific professional journals.

5. Fine-Tuning Platform for Bioinformatics Repositories

Aiming to develop a platform to fine-tune ChatGPT with bioinformatics repositories, enhancing query results for newer tools.

📫 Connect with me