In this 3-hour workshop, we will use R to analyze DNA variants from Variant Call Format files to identify those likely to have a functional impact. It is intended for those with intermediate R programming skills.

Offered biannually.

Course website and materials

In this 3-hour workshop, we will use R for annotating genomic data with information from various reference genome and functional databases. It is intended for those with intermediate R programming skills.

Offered biannually.

Course website and materials

In this 3-hour workshop, we will use R to analyze bulk RNA-seq data to perform differential expression analysis, enrichment analysis, and visualizations. It is intended for those with intermediate R programming skills.

Offered biannually.

Course website and materials

In this 3-hour workshop, we will demonstrate how to process and analyze single cell RNA-seq data using R Bioconductor packages, focusing primarily on seurat. It is intended for those with intermediate R programming skills who are familiar with the biological concepts of single cell RNA-seq.

Offered biannually.

Course website and materials

The learning objectives for this 3-hour workshop include

1. How to go from a matrix of raw gene expression counts to differentially expressed genes.
2. How to analyze experimental designs that go beyond 2-group comparisons using edgeR’s generalized linear modeling capabilities.
3. Ways to test specific hypotheses using a joint model fit. Prerequisites: A minimum of 4-6 months experience programming in R and have taken the RNAseq Analysis in R workshop or something equivalent.
   Intro to RNA-seq analysis

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. To quantify the expression levels, RNA-seq has become one of the most popular experimental methods. This workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data analysis steps for recovering actionable insights. Attendees will learn to explore and understand RNA-seq data using Galaxy — an easy-to-use web-based platform. No data analysis or RNA-seq experience is required.

During this 1-day, hands-on workshop, we will cover techniques, platforms and methods that are used in analyzing single cell data. The workshop has two hands-on sessions: an introductory session in the morning and a more advanced session in the afternoon.

Morning session: analysis using Cellranger and Seurat.

Afternoon session: three consecutive advanced hands-on sessions ranging from network analysis of single cell datasets in Cytoscape, normalization and differential analysis outside of Seurat and querying a Single Cell Atlas for cell types.

During this 1-day symposium, we will cover techniques, platforms and methods that are used in analyzing single cell data. The symposium has two sessions: a series of seminars in the morning and hands-on workshops in the afternoon.

Morning session: introduction of single cell platforms, followed by talks focusing on applications of various technologies to diverse research areas.

Afternoon session: three consecutive hands-on sessions with increasing difficulties, ranging from how to use Cell Ranger and Seurat to advanced analyses beyond these common tools.

This 3-hour workshop will be both theoretical and hands-on. We will learn the main tools used to do alignment, variant calling, annotation and visualization. We will start with raw FASTQ reads and get to annotated variants (VCF files).

Week 1: Human Genome Structure, Function and Variation
Video:  Part 1 | Part 2 | Part 3 | Part 4 | Part 5
Slides:  Download

Week 2: Mendelian Diagnostic Testing
Video:  Part 1 | Part 2 | Part 3 | Part 4 | Part 5
Slides:  Download Part A |  Download Part B | Download Supplement

Week 3: Next-gen Sequencing for Diagnostic Dilemmas
Video:  Part 1 | Part 2 | Part 3 | Part 4
Slides:  Download

Week 4: Methods for Dissecting the Genetic Basis of Complex Diseases
Video:  Part 1 | Part 2 | Part 3 | Part 4 | Part 5
Slides:  Download

Week 5: Predictive Testing for Common, Complex Diseases
Video:  Part 1 | Part 2 | Part 3 | Part 4
Slides:  Download

Week 6: Pharmacogenomics
Video:  Part 1 | Part 2 | Part 3 | Part 4
Slides:  Download

Week 7: Cancer Genomics
Video:  Part 1 | Part 2 | Part 3 | Part 4
Slides:  Download