Welcome to High-throughput Biology - From Sequence to Networks 2019.
The course schedule can be found here
If you have questions or comments, visit the workshop Q&A forum. You may need to join the group by clicking on the “+” symbol and entering the class code.
You can download the printed course manual here.
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.
- The CBW R tutorial
- Quick and Dirty Guide to R
- The R Tutorial up to and including 5. Basic Plots
- The R command cheat sheet
2) UNIX Preparation tutorials:
4) Cytoscape Preparation tutorials: Complete the introductory tutorial to Cytoscape
Introduction to Cytoscape3 - User Interface
Introduction to Cytoscape3 - Welcome Screen
Filtering and Editing in Cytoscape 3
Before coming to the workshop, read these:
Module 1: Introduction to High-throughput Sequencing
Module 2: Data Visualization
Module 3: Genome Alignment
- We have set up 30 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.
Module 4: Small-Variant Calling and Annotation
Module 5: Structural Variant Calling
Module 6: De Novo Assembly
Day 3 and Day 4 refer to content in the RNA-Seq wiki.
Module 7: Introduction to RNA Sequencing Analysis
Module 8: RNA-seq Alignment and Visualization
Module 9: Expression and Differential Expression
Module 10: Reference Free Alignment
Module 11: Isoform Discovery and Alternative Expression
Keeping Up-to-date with RNA-Seq Analysis Developments
For additional resources, tutorials, future directions, and more please refer to the RNA-seq wiki
Module 12: Introduction to Pathway and Network Analysis
Module 13: Finding Over-Represented Pathways
Module 13 Lab Practical: Enrichment-Based Analysis - Performing ORA
Jüri Reimand and Veronique Voisin
Module 14: Network Visualization and Analysis with Cytoscape and Reactome
Module 14 Lab Practical: De novo subnetwork clustering analysis - Reactome
Module 15: More Depth on Network and Pathway Analysis and Cytoscape Enrichment map
Module 15 Lab Practical: Cytoscape-Enrichment Map
Module 16: Gene Function Prediction
Module 17: Regulatory Network Analysis
Module 17 Lab Practical: iRegulon
To use the precomputed results:
1) launch Cytoscape
2) open the “prostate_cancer_genemania_network.cys” file
3) go to App > iRegulon > ‘Load results from the iregulon_results.irf file’