Computational Genomics, November 30 - December 7, 2022

Participating Faculty

Group Photo

Helpful links, analysis scripts and other software notes

Additional analysis tutorials in Galaxy -- via Galaxy Training Network

30 Nov. Wednesday
9:00 Introduction and Overview Hawkins/Mills/Pearson
9:30 Protein Evolution and Sequence Similarity Searching Pearson
Sign up for AnVIL
Register with Google linked email address which can be a non-gmail account if you fist link it with Google.
Update spreadsheet
11:00 Workshop: Similarity searching and statistics
 
1:30 Safety Lecture / Workshop Discussion
2:00 Practical Sequence Similarity Searching Pearson
3:15 Workshop: Advanced alignment; scoring matrices
4:30 Poster Session/Wine and Cheese
 
7:30 Workshop/Project discussion
8:30 Galaxy 101 - Using Galaxy for reproducible analyses Collins
Exercise
1 Dec. Thursday
9:00 Galaxy Intro Try 2 - same as last night
10:00 RNA sequencing Mills
11:00 Workshop -- Transcriptomics with Galaxy Mills
 
1:30 Discussion
2:00 Intro to genomic sequencing technology the short and long of it all Miller
3:30 PSSMs and HMMs - customized scoring matrices Pearson
5:00 Workshop -- Transcriptomics with Galaxy Mills
 
7:00 Pick your project and start discussing data and sketching out a question
2 Dec. Friday
9:00 Discussion
9:30 Intro to R and Reproducibility in Analysis Hicks (remote)
More about R Projects and how to organize analysis
More about Tidy data (making data that works with ggplot2)
11:00 Workshop - Doing fun stuff with R Hicks
11:45 Course Photo
 
1:30 Scaling up single-cell and spatial genomic data science Hicks (remote)
3:45 Workshop Fun stuff with 'R' (cont.) Hicks (remote)
 
6:00 Pizza in Hershey
 
7:00 Unix set up for bedtools workshop
7:30 Introduction to genome intervals, genome arithmetic, and bedtools Quinlan (remote)
9:00 Workshop - bedtools tutorial and puzzles
3 Dec. Saturday
9:00 Analyzing Single-cell data - PHATE/Multiscale PHATE/MELD Krishnaswamy
11:00 Workshop -- Single cell analysis
 
1:30 Discussion
2:00 IGV for visualizing sequencing data Miller
2:30 Long read sequencing Miller
3:30 Accessing public sequence datasets Mills
5:00 Student projects
 
7:30 Student project update
8:30 Mid-term exam
4 Dec. Sunday
9:00 Mid-term review
10:30 Single Cell analysis II - MAGIC/ Pseudo time and Trajectory Net Krishnaswamy
 
1:30 Discussion
2:00 Discovery and analysis of genetic variation Quinlan (remote)
3:10 More genetic variation Quinlan (remote)
4:00 Single Cell Workshop II
 
7:30 Student projects
5 Dec. Monday
9:00 Regulatory Genomics Hawkins
10:30 Chromatin States 1: Analysis of Histone Modifications Hawkins
 
1:30 Discussion
2:00 Special Seminar - Manifolds, flows and dynamics of single cell data, Wendt Building
 
3:15 Discussion
3:30 Workshop: Annotating ChIP Peaks in Galaxy
Workshop:ATAC-seq Peak Calling in Galaxy
 
6:00 Banquet
6 Dec. Tuesday
9:00 Chromatin States 2: Overlapping Datasets Hawkins
10:30 Probing higher dimension chromatin structure Hawkins
 
1:30 Discussion
2:00 Gene Lists to Pathways Moss
MultiPLIER: another way to get pathway information from your expression datasets
3:30 Optional Workshop time. You can use this time to try ORA with gene lists, catch up on other workshops from the course, and/or work on projects.
Workshop - ORA
Expression Results for workshop (ORA_results.tabular)
ORA tools
 
3:30 CSHL Tour - Grace Auditorium
4:30 Student Projects
 
7:30 Student Projects
7 Dec. Wednesday
9:00 Student Projects -- Final Presentation Students
11:30 Course Overview/Discussion
12:00 Farewell

Last updated: via Google Docs