Prostate Cancer Translational Research Hub

Empowering clinicians and researchers with cutting-edge bioinformatics tools that bridge the gap between bedside, bench, and bytes.

4 Web Tools
2,000+ Cell Lines
500+ Omics Samples
Siyuan Cheng

About Me

I am a computational biologist and aspiring physician-scientist with a passion for developing AI-driven platforms to improve prognosis and overcome therapeutic resistance in prostate cancer. My research focuses on building foundational 'big-data' resources, developing novel AI models to interpret these datasets, and validating these findings experimentally.

Open Research Data

Access raw data and processed files from our publications via Figshare. All datasets are freely available for the research community.

CTPC Raw Data

1,840 prostate cancer cell line samples with comprehensive RNA-seq data for precision medicine research.

Raw count matrices
Processed data files
Clinical metadata
View Dataset

HuPSA & MoPSA

Single-cell RNA-seq objects in Seurat V5 format for human and mouse prostate cancer atlases.

Human prostate atlas
Mouse prostate atlas
Ready-to-use R objects
View Dataset

LNCaP-ADT Multi-Omics Bundle

Complete multi-omics dataset for androgen deprivation therapy resistance research (500+ samples across multiple timepoints).

RNA-seq Data
View on Figshare
ATAC-seq BigWigs
View on Figshare
ChIP-seq BigWigs
View on Figshare
Raw Heatmaps
View on Figshare
TF Peaks
View on Figshare
Chromatin Peaks
View on Figshare

Interactive Web Applications

Our web-based tools provide intuitive access to complex multi-omics datasets.

HuPSA-MoPSA

pcatools.shinyapps.io/HuPSA-MoPSA

Single-Cell Atlas Explorer. Navigate the cellular landscape of prostate cancer with unprecedented detail through our comprehensive single-cell RNA sequencing atlas.

Discover Novel Biomarkers
Uncover hidden cellular populations linked to aggressive disease progression.
Clinical Translation
Validate subtype markers across 50+ bulk transcriptome datasets.
HuPSA-MoPSA Interface Preview

CTPC

pcatools.shinyapps.io/CTPC_dev

Prostate Cancer Cell Line Encyclopedia. Optimize your research model selection with comprehensive molecular profiling of 2,000+ prostate cancer cell lines.

Golden-Standard Baselines
Access molecular profiles of established cell lines (LNCaP, PC3).
Treatment-Gene Networks
Identify drug-responsive pathways for mechanistic studies.
CTPC Interactive Demo

LNCaP-ADT Hub

pcatools.shinyapps.io/shinyADT

Deciphering Resistance Mechanisms. Explore the molecular evolution of treatment resistance through integrated multi-omics analysis.

Multi-Omics Integration
Correlate transcriptomic, epigenetic, and TF occupancy data.
Dynamic Adaptation Maps
Track molecular changes during ADT at single-cell resolution.
LNCaP-ADT Analysis Interface

PCTA Atlas

pcatools.shinyapps.io/PCTA_app

Pan-Cancer Transcriptome Atlas. Compare prostate cancer biology with 535+ cell lines across 114 cancer types.

Cross-Cancer Insights
Dataset spanning 24,965 genes across 84,385 samples.
Biomarker Discovery
Validate prostate cancer-specific markers across cancer types.
PCTA Pan-Cancer Analysis Interface

Computational Pipelines

AI-powered research assistants that streamline complex analytical tasks.

IMPACT-sc

github.com/schoo7/impact_sc

Integrated Single-Cell Analysis Pipeline. A comprehensive pipeline for single-cell transcriptomics analysis, integrating data processing and annotation.

Modular Architecture
10+ analysis modules from QC to advanced downstream analyses.
AI-Powered Annotation
Integrates Cell2Sentence for semantic cell type prediction.
Python R Single-Cell

SRA-LLM

github.com/schoo7/SRA_LLM

Smart Research Assistant. An intelligent research assistant leveraging Large Language Models to accelerate literature review.

LLM Integration
Powered by state-of-the-art language models for literature analysis.
Knowledge Integration
Connects findings across studies to reveal hidden patterns.
LLM NLP AI Assistant