A catalog of common issues when working on the Jupyter Hub can be found here.
Classes are held from 8:30 AM to 5:00 PM (central time).
| LIVE CONTENT | ||||||
|---|---|---|---|---|---|---|
8:30-8:45AM | 8:45-9:45AM | 10-10:30AM | 10:30AM-12:15PM | 1:15-2:45PM | 3:00-5:00PM |
|
6/24 | Welcome & Introduction | Genome Assembly Chris Fields (lecture) | Lab Introduction | Genome Assembly Lab (self-paced) | Polymorphisms & Association Tests Alex Lipka pdf | pptx (lecture) | Polymorphisms & Association Tests Lab (synchronous) |
8:30-10AM | 10:15AM-12:15PM | 1:15-2:45PM | 3:00-5:00PM |
|
6/25 | Clinical Variant Interpretation Joe Farris (lecture) | Clinical Variant Interpretation Lab Joe Farris (synchronous) | Bulk RNA-Sequencing Analyses Jessica Holmes (lecture) | Bulk RNA-Sequencing Analyses Lab (self-paced) |
8:30-10:30AM | 10:45AM-12:15PM | 1:15-2:45PM | 3:00-5:00PM |
|
6/26 | RNA-Seq in Hereditary Disease Diagnosis Collin Osborne (lecture & lab) | Microbiome Bionformatics Lu Yang, Jun Chen (lecture) | Basic Single Cell & Spatial Transcriptomics Jenny Drnevich (lecture) | Basic Single Cell & Spatial Transcriptomics Lab (self-paced) |
8:30-10AM | 10:15AM-12:15PM | 1:15-2:45PM | 3:00-5:00PM |
|
6/27 | Clinical Single Cell & Spatial Transcriptomics Yan Asmann (lecture) | Clinical Single Cell & Spatial Transcriptomics Lab (self-paced) | Regulatory Genomics Charles Blatti (lecture) | Regulatory Genomics Lab (self-paced) |
6/28 | Exploring AI Priyam Mazumdar (lecture) | Exploring AI Lab Priyam Mazumdar (synchronous) | Clinical Applications of AI Irbaz Riaz, YooJung Choi, Kenneth Kehl (lecture) | Clinical Applications of AI Lab Umair Ayub, Syed Naqvi, Mihir Parmar (synchronous) |
BREAKS
Monday | 9:45-10AM
Wednesday | 10:30-10:45AM
Tuesday, Thursday, & Friday | 10-10:15AM
Lunch break | 12:15-1:15PM daily
PM break | 2:45-3PM daily
| ON DEMAND CONTENT | ||
|---|---|---|
| Variant Calling Chris Fields (lecture) | Systems Biology Charles Blatti (lecture) |
|
Pre-Course Requirements
Please spend some time familiarizing yourself with the programs we will be using in the course.
RNA-Seq in Hereditary Disease Diagnosis lab session requires a google account to participate. If you do not already have a Google account you will need to sign up for one. Setting up an account is quick and easy and can be done here: https://www.google.com/account/about/.
Tutorials & Optional Background Reading
RStudio: http://tryr.codeschool.com/ ; http://www.r-tutor.com/r-introduction
For the Clinical Variant Interpretation Module:
Overview of Specifications to the ACMG/AMP Variant Interpretation Guidelines
https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cphg.93
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
https://www.nature.com/articles/gim201530
For additional information on R and RStudio:
https://moderndive.netlify.pp/1-getting-started.html
For the module on “RNAseq in Hereditary Disease Diagnosis”:
Improving genetic diagnosis in Mendelian disease with transcriptome sequencing:
https://stm.sciencemag.org/content/9/386/eaal5209.short
OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data:
https://www.sciencedirect.com/science/article/pii/S0002929718304014
LeafCutterMD: an algorithm for outlier splicing detection in rare diseases:
https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btaa259/5823301
A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease:
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223337