Intro to Single Cell RNA-Seq:
Spring 2021 Advanced Bootcamp

Welcome to Bioinformatics Bootcamp Advanced Topics: Intro to Single Cell RNA-Seq!

This page contains all the lectures and materials needed to participate. 

For any questions, please contact Henry Miller (Email in Syllabus). You can also stop by Henry's office hours whether or not you are enrolled. 

Github Workshop Repo HERE
Download the Syllabus HERE

Module #1: Orientation and getting started with scRNA-Seq

In this lecture, we give an overview of the workshop and a brief background on bulk RNA-Seq and scRNA-Seq. Finally, we demonstrate how to load single cell datasets into R.

Lecturer: Henry Miller

Date/time: Feb 9th, 2021 (5PM CST)

 

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Find a new scRNA-Seq study from 10X (link) and load it into R using Seurat. Due by Module #2 (Feb 16th)

Module #2: scRNA-Seq data preparation and QC

In this lecture, we give an overview of the upstream processing pipeline for scRNA-Seq (cellranger). We will also demonstrate how to perform basic QC and normalization of scRNA-Seq datasets. Finally, we discuss the ways to get single cell datasets from various sources into Seurat.

Lecturer: Henry Miller

Date/time: Feb 16th, 2021 (5PM CST)

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Complete the activities in the module_2.R script. 

Module #3: Uncovering dataset structure

In this lecture, we give an overview of the process of uncovering dataset structure in scRNA-Seq. 

Links I mentioned during the video:

1. PCA on StatQuest (link)

2. PCA web app (link)

3. UMAP web app (link)

4. Nearest Neighbors on StatQuest (link) -- they explain it in the context of KNN classifiers, but this is the same intuition for how nearest neighbors work in graphs. 

Lecturer: Henry Miller

Date/time: Feb 23rd, 2021 (5PM CST)

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Complete the activities in the module_3.R script. 

Module #4: Biological Interpretation

In this lecture, we give an overview of the process of interpreting scRNA-Seq in a biological context. 

Links:

- Enrichr: HERE

- Tabula Muris Paper: HERE

Lecturer: Henry Miller

Date/time: Mar 2nd, 2021 (5PM CST)

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Complete the activities in the module_4.R script. 

Module #5: Advanced Topics

In this lecture, we discuss advanced topics in scRNA-Seq analysis, including (1) data integration, (2) module scoring, and (3) trajectory analysis.

Links:

- SCTransform paper: HERE

Lecturer: Henry Miller

Date/time: Mar 9th, 2021 (5PM CST)

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Complete the activities in the module_5.R script. 

Module #6: Advanced Topics II

In this lecture, we discuss additional advanced topics in scRNA-Seq analysis, including (1) differential state analysis and (2) graph signal processing.

Lecturer: Henry Miller

Date/time: Mar 16th, 2021 (5PM CST)

**Note**

Some user's had an error this time:

Error: package or namespace load failed for ‘Seurat’:  

         object ‘markvario’ is not exported by 'namespace:spatstat'

The fix was to reinstall the development version of Seurat:

remotes::install_github(repo = 'satijalab/seurat', ref = 'develop')

Post-doc positions:

1. BIGGs institute: LINK

Bioinformatics Research Network:

This is a network for remote collaboration on bioinformatics-based research projects. You can join as a project 'owner' (host a project) or as a project 'volunteer' (join a project). 

We currently have 20 projects and 142 volunteers in the network.

If you want to sign up, please fill out our signup form: LINK

Other links:

1. Krishnaswamy lab: LINK

2. PHATE paper: LINK

3. MAGIC paper: LINK

4. scRNA-tools: LINK

5. AD paper: LINK

6. AD paper shiny app: LINK

7. SuperExactTest: LINK

Materials:

- Slides: HERE

- Github Repository (Scripts and Data): HERE

Activity/Homework

Complete the optional project (LINK) any time.