Short Courses & Workshops

Short Courses & Workshops

LIBRARY BIOINFORMATICS WORKSHOPS

Data Science Initiative website

DNA Variant Analysis with R Bioconductor

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

Genomic Annotations with R Bioconductor

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

RNA-Seq Analysis with R Bioconductor

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

Single-cell RNA-seq Analysis with Bioconductor

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

BAKAR INSTITUTE / GLADSTONE INSTITUTE WORKSHOPS

Bakar Computational Health Sciences Institute (BCHSI) website
See Education and Events for current listings

Intermediate R: RNAseq Analysis

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.

Single Cell Analysis Hands-on Workshop

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.

Single Cell Technology & Analysis Symposium

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.

Workshop on Whole Genome & Exome analysis

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).

GENOMIC & PRECISION MEDICINE ONLINE COURSE

This course aims to provide participants with some baseline knowledge of genomics, an overview of the clinical applications of genomic medicine, the skills to evaluate the clinical validity and utility of new tests, and an appreciation of the associated ethical and social issues inherent in this field.

Content presented by Robert Nussbaum, MD and Jeanette McCarthy, PhD.

Course Content — Genomic & Precision Medicine

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