Schedule - Spatial Transcriptomics

Pre-reading

  1. Spatial Technology Overview
  2. Space Ranger Summary
  3. Download Project

Day 1

Time Topic Instructor
10:00 - 10:15 Workshop Introduction Instructor_name
10:45 - 11:45 Introduction to Spatial Transcriptomics Dr. Mandovi Chatterjee
10:45 - 10:50 Break
10:50 - 11:25 Load Visium HD Data Instructor_name
11:55 - 12:00 Overview of self-learning materials and homework submission Instructor_name

Before the next class:

I. Please study the contents and work through all the code within the following lessons:

  1. Principal Component Analysis (PCA)

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3

  2. Quality Control

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3
  1. Submit your work:
  • Each lesson above contains exercises; please go through each of them.
  • Submit your answers to the exercises using this Google form on the day before the next class.

Questions?

  • If you get stuck due to an error while running code in the lesson, email us

Day 2

Time Topic Instructor
10:00 - 10:30 Self-learning lessons discussion All
10:30 - 10:55 Normalization and Sketch Downsampling Instructor_name
10:55 - 11:00 Break
11:00 - 11:55 Dimensionality Reduction Instructor_name
11:55 - 12:00 Overview of self-learning materials and homework submission Instructor_name

Before the next class:

I. Please study the contents and work through all the code within the following lessons:

  1. Clustering

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3

  2. Integration

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3

  3. Seurat Cheatsheet

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3
  1. Submit your work:
  • Each lesson above contains exercises; please go through each of them.
  • Submit your answers to the exercises using this Google form on the day before the next class.

Questions?

  • If you get stuck due to an error while running code in the lesson, email us

Day 3

Time Topic Instructor
10:00 - 10:30 Self-learning lessons discussion All
10:30 - 10:55 BANKSY Spatial Clustering Instructor_name
10:55 - 11:00 Break
11:00 - 11:55 Deconvolution Instructor_name
11:55 - 12:00 Overview of self-learning materials and homework submission Instructor_name

Before the next class:

I. Please study the contents and work through all the code within the following lessons:

  1. Differential Expression and Pathway Analysis

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3

  2. Spatially Variable Genes

    Brief description of the lesson.

    In this lesson, you will:

    • Learning Objective 1
    • Learning Objective 2
    • Learning Objective 3
  1. Submit your work:
  • Each lesson above contains exercises; please go through each of them.
  • Submit your answers to the exercises using this Google form on the day before the next class.

Questions?

  • If you get stuck due to an error while running code in the lesson, email us

Day 4

Time Topic Instructor
10:00 - 10:30 Self-learning lessons discussion All
10:30 - 11:25 Cell-Cell Communication Instructor_name
11:25 - 11:30 Break
11:30 - 11:45 Discussion, Q & A Instructor_name
11:45 - 12:00 Wrap Up Instructor_name

Resources