Schedule

6/29/2023

• 12:00-19:00
  Students arriving
  Students arriving –

• 19:00-20:30
  Introductions
  Introductions –
  informal discussion

6/30/2023

• 9:00-12:00
  Introduction to R
  Introduction to R – Sean
  Sean
  lecture/lab

• 13:00-14:00
  Probability and simulation
  Probability and simulation – Vince
  Vince
  lecture

• 14:00-17:00
  EDA and visualization
  EDA and visualization – Vince
  Vince
  lecture/lab

• 19:00-21:00
  Student talks
  Student talks – Students
  Students
  chalk talk or 3 slides

7/1/2023

• 9:00-10:30
  Introduction to R
  Introduction to R – Sean
  Sean
  lecture/lab

• 10:30-12:00
  Inference, p-values, FDR
  Inference, p-values, FDR – Vince
  Vince
  lecture

• 13:00-15:00
  t-statistic and basic power calculations
  t-statistic and basic power calculations – Sean
  Sean
  lecture/lab

• 15:00-17:00
  Overview of Bioconductor
  Overview of Bioconductor – Vince
  Vince

• 19:00-21:00
  Student talks
  Student talks – Students
  Students

7/2/2023

• 9:00-10:30
  Public Data and Data Access
  Public Data and Data Access – Sean
  Sean
  Lecture

• 10:30-12:00
  Rmarkdown
  Rmarkdown – Sean
  Sean
  Lecture/lab

• 13:00-14:30
  Linear regression and GLMs
  Linear regression and GLMs – Vince
  Vince
  Lecture/lab

• 14:30-17:00
  Summarized Experiment
  Summarized Experiment – Sean
  Sean
  Lecture/lab

7/3/2023

• 9:00-11:00
  SummarizedExperiment objects in the real world
  SPEAQeasy / smokingMouse introduction
  Leo, Daianna, Renee (aka, Leo’s team)
  Lecture/lab

• 11:00-12:00
  Interactive SummarizedExperiment visualizations
  Visualization of expression data with iSEE + mean/centering heatmaps
  Leo
  Lecture/lab

• 13:00-14:00
  Overview of smokingMouse plots + hands-on exercise overvview
  Daianna (lead), Leo (support)
  Lecture/lab

• 14:00-17:00
  Hands-on exercise to reproduce smokingMouse plots with iSEE & R
  NA (Leo’s team)
  lab

• 19:00-20:00
  biocthis: making your R/Bioconductor package
  Introduction to making R/Bioconductor packages with biocthis
  Leo
  demo

7/4/2023

• 9:00-11:00
  SummarizedExperiment objects built with recount3
  Downloading RNA-seq data using recount3
  Leo
  Lecture/lab

• 11:00-12:00
  Interpreting coefficients
  Statistical models with ExploreModelMatrix
  Leo
  Lecture/lab

• 13:00-14:00
  DE analysis main steps
  Differential expression analysis introductory code with limma + hands-on exercise overview
  Leo
  Lecture/lab

• 14:00-17:00
  hands-on exercise using recount3 data
  NA (Leo’s team)
  lab

• 19:00-23:59
  Off for fireworks
  Off for fireworks – NA
  NA

7/5/2023

• 9:00-10:30
  Model building
  Choosing variables for your DE analysis with variancePartition
  Daianna (lead), Leo (support)
  Lecture/lab

• 10:30-12:00
  Expression heatmaps
  Visualizing DE genes with ComplexHeatmap
  Renee (lead), Leo (support)
  Lecture/lab

• 13:00-14:30
  Bayes Theorem
  Tomas

• 15:00-17:00
  hands-on portion of variancePartition + ComplexHeatmap with smokingMouse / recount3 / their data
  NA (Leo’s team)
  lab

• 19:00-20:00
  Anything the students wants (more biocthis? HubPub demo?)
  Leo
  demo

7/6/2023

• 9:00-10:00
  Visium spatial overview
  Introduction to the world of spatially-resolved transcriptomics with Visium data (SingleCellExperiment –> SpatialExperiment –> spatialLIBD)
  Leo
  Lecture

• 10:00-12:00
  spatialLIBD overview
  Downloading public Visium spatial data with spatialLIBD + visualizing it with it (shiny app + R functions)
  Leo
  Lecture/lab

• 13:00-14:30
  Dimensional Reduction
  Tomas

• 14:30-15:30
  spatialLIBD functions for pseudobulking & DE
  spatialLIBD: re-use of bulk RNA-seq methods for spatial data (pseudobulk + PCA) + hands-on exercise overview
  Leo
  Lecture/lab

• 15:30-17:00
  Hands-on with making plots with pseudobulked spatial data (3 LIBD projects to choose from)
  NA (Leo)
  lab

7/7/2023

• 0:00-23:59
  Day off
  NA

7/8/2023

• 9:00-12:00
  Min

• 13:00-17:00
  GSEA
  Ludwig

7/9/2023

• 9:00-12:00
  Min

• 13:00-17:00
  Min

7/10/2023

• 9:00-16:00
  Motif discovery lecture/lab
  Harmen

• 16:00-17:00
  Research Talk
  Dissecting cis-regulatory logic with deep sequencing and biophysically interpretable machine learning
  Tomas

• 19:00-20:00
  Research Talk
  Inferred transcription factor activity as a quantitative genetic traiit
  Harmen

7/11/2023

• 9:00-11:00
  ATAC-Seq
  ATAC-Seq – Sean
  Sean

• 11:00-12:00
  Machine Learning
  Machine Learning – Sean
  Sean

• 13:00-14:00
  Machine Learning
  Machine Learning – Sean
  Sean

• 14:00-17:00
  ML or ATAC lab
  ML or ATAC lab – Sean
  Sean

7/12/2023

• 9:00-12:00
  Motif discovery lecture/lab
  BANQUET
  Harmen

• 13:00-16:00
  Open Lab
  Open Lab – NA
  NA

• 18:00-21:00
  BANQUET
  BANQUET

7/13/2023

• 00:00-24:00
  DEPARTURE
  DEPARTURE