Supplementary Datasets and Tutorial Video for TiRank: Prioritizing phenotypic niches in tumor microenvironment for clinical biomarker discovery

Overview This repository contains the supplementary testing datasets and the tutorial video for TiRank, a computational tool designed to prioritize phenotypic niches in the tumor microenvironment for clinical biomarker discovery. These resources support the manuscript and software documentation, facilitating reproducibility of the analysis pipelines. Repository Content 1. Test Datasets (ExampleData)This dataset allows users to reproduce the TiRank example workflows (Single-cell classification and Spatial Transcriptomics survival analysis). It includes processed data aligned with the software's tutorials: Melanoma (SKCM) Dataset: Used for scRNA-seq to Bulk integration (Response prediction). GSE120575.h5ad: Single-cell RNA-seq data (H5AD format). Liu2019_exp.csv: Bulk RNA-seq expression matrix. Liu2019_meta.csv: Clinical metadata for bulk samples. Colorectal Cancer (CRC) Dataset: Used for Spatial Transcriptomics to Bulk integration (Prognosis prediction). SN048_A121573_Rep1/: Spatial transcriptomics data folder. GSE39582_exp_os.csv: Bulk expression data with survival outcomes. GSE39582_clinical_os.csv: Clinical metadata. 2. Tutorial VideoA comprehensive video guide demonstrating the usage of the TiRank Web GUI and analysis workflow. 3. Pre-trained CTransPath ParametersCheckpoint file for pre-trained CTransPath model. Software Availability The TiRank software source code is available on GitHub: https://github.com/LenisLin/TiRank