Lecture 4: Result Validation at Tissue-level using TCGA Public Resource

↩︎️ Lecture Material


Lecture Description

The final class will consist of validating the results from scRNA-seq data analysis using TCGA gastric adenocarcinoma bulk dataset. The class will cover from accessing the TCGA public database directly from R to data exploration via UCSCXenaTools and normalization to correction of clinical covariates via survival and visualization using Kaplan-Meier survival curves. Moreover, performing TCGA data analysis (e.g. Differential Expression Analysis and Gene set variation analysis on tissue level) outside of RStudio and via the UCSC Xena Browser (Web tool) will be introduced in class as well.

Own Preparation

1. Revisit previous lectures (required) Prior to attending the lecture, we highly recommend that participants spend time reviewing lectures 1 through 3.

2. Prepare Your R Environment (recommended) For the practical session of Lecture 4,

IMPORTANT: Install the following R packages prior to this class:
- UCSCXenaTools
- biomaRt
- survival

3. Review the Paper (recommended) The following paper serves as the foundation reference for the analysis conducted during the course: Single-cell landscape reveals active cell subtypes and their interaction in the tumor microenvironment of gastric cancer

4. Take advantage of free tutorials online on TCGA analysis. (recommended) We recommend that participants familiarize themselves with USCS Xena Platform: