Workshop Description (Intermediate Course)

As we step into the era of precision medicine, the need for extensive genomic data analysis is more pressing than ever. With the advent of high-throughput technologies, a plethora of genomic, transcriptomic, and epigenomic datasets from cancer patients have been sequenced, providing a wealth of data for systematic bioinformatics analysis. This workshop is tailored to assist cancer bioinformaticians, postdoc researchers, and graduate students who are interested in incorporating expansive cancer genomic datasets from an open-source platform – The Cancer Genome Atlas (TCGA) – into their research.
 Enrolled participants will gain insights into the fundamental principles of TCGA, including the different data categories and structures, methods for downloading data, and basic pipelines for data analysis within the TCGA platform. The workshop will also provide a versatile R script scaffold for mining TCGA datasets, empowering attendees to analyze their own unique cohorts of cancer genomic datasets.

 

Workshop Materials

Day I: Introduction and Data Downloading Guide
A. Overview of TCGA
B. Navigating the diverse datasets within TCGA
C. Methods for data mining
D. Understanding TCGA’s barcode system
Day II: Utilizing the R Package TCGAbiolinks
A. Introduction to the TCGAbiolinks package
B. The three primary functions of TCGAbiolinks: data query, download, and preparation
C. Hands-on practice: downloading data using TCGAbiolinks
Day III: Data Analysis
A. TCGAanalyze: analyze data from TCGAbiolinks pipeline
B. Differential gene expression analysis with DESeq2
C. Dimensionality reduction and clustering via Uniform Manifold Approximation and Projection (UMAP)

Technical Requirements

TBD

Instructor

Dr. Xianglong Tan is a postdoctoral researcher in Dr. Michael Carey’s Lab at UCLA. He earned his Ph.D. from Tsinghua University, focusing on protein regulation via post-translational modifications. At the Carey Lab, Xianglong’s research delves into how gene transcription is influenced by enhancers through 3D genome interactions, and how these aberrant interactions can lead to oncogenic expression in lung cancer.

 

Videos

Reviews

Workshop Details

Prerequisites: Intro to Unix Command Line (W1) and Intro to R (W3) is highly recommended.
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Boyer Hall, 529
Seats Available: 28

Winter 2024 Dates

Mar 5, 6 and 7
1:30 PM – 4:30 PM

REGISTRATION IS OPEN!