https://github.com/cafferychen777/cafferychen777
https://github.com/cafferychen777/cafferychen777
Last synced: 8 months ago
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- Host: GitHub
- URL: https://github.com/cafferychen777/cafferychen777
- Owner: cafferychen777
- Created: 2023-10-06T07:10:50.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-02-16T07:12:57.000Z (9 months ago)
- Last Synced: 2025-02-16T08:19:03.515Z (9 months ago)
- Size: 57.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
[](https://github.com/cafferychen777/github-readme-stats)
📊 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.
## 🎖 Achievements
- Awarded the **Inaugural Su Binghua Distinguished Biostatistics Scholarship** ($2,800) by Tigermed, 2024
- Only undergraduate recipient among PhD candidates across mainland China
- 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**](https://scholar.google.com/citations?user=gonDvdwAAAAJ&hl=en) at Mayo Clinic, my research primarily revolves around microbiome data analysis.
- Developed the [**MicrobiomeStat R package**](https://github.com/cafferychen777/MicrobiomeStat), writing **over 17,000 lines of R code**. Comprehensive documentation is available on the [**package wiki**](https://www.microbiomestat.wiki/), which contains in-depth guidance and tutorials exceeding **20,000 words**. Additionally, an interactive [**MicrobiomeStat Shiny application**](https://microbiomestat.shinyapps.io/MicrobiomeStat-Shiny/) has been created to provide a user-friendly platform for longitudinal statistical analysis and visualization of microbiome data.
- Pioneered the [**MicrobiomeGallery**](https://a95dps-caffery-chen.shinyapps.io/MicrobiomeGallery/) collaborative platform.
- Independently developed the [**ggpicrust2**](https://github.com/cafferychen777/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 very **open to collaborations**, especially in the areas of multi-omics, single-cell, spatial transcriptomics, and microbiome data analysis. If you have any projects in these fields and think we could collaborate, please feel free to reach out! I am also eager to assist others with their data analysis needs in these areas.
Additionally, I am particularly interested in collaborating with researchers who have used my tools, such as **ggpicrust2** or **MicrobiomeStat**. If you're considering using or have already incorporated these tools into your research, we can explore potential co-authorship opportunities. Whether it's data analysis, interpretation, or manuscript preparation, I'm happy to contribute my expertise. Let’s work together to advance these fields!
## 🛠 Projects
#### 1. LLMCal - AI-Powered Calendar Event Creator
A PopClip extension that leverages Claude AI to intelligently convert selected text into calendar events, automatically extracting meeting details, times, and locations. The tool understands natural language and seamlessly integrates with macOS Calendar.
#### 2. 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.
#### 3. 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.
#### 4. 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.
#### 5. PI_find
A tool designed to assist graduate school aspirants in discovering PI names from specific professional journals.
#### 6. 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
[](https://twitter.com/CafferyYang)