Daily task list and todos

The materials are still evolving, while you can continue on ahead, you may need to backtrack and redo some materials as I may have changed them.

Monday, July 18

Monday’s goal is introductions, setup and prerequisites

My intro Day 1 YouTube Video

1. Introduce yourselves to each other and to the instructors.
2. Post an introduction of yourself onto the Discussion Page.
3. Read over the welcome page (Very Short).
4. If needed install the most current versions of R AND RStudio, please do so.
5. Review the UCD Intro to R course.
   • this course is a 1.5-day course, however the intent here is to review the materials and not do everything.
   • I assume you all have experience and if anything just need a refresher.
6. Perform the “scRNAseq Analysis” section. Prepare your RStudio environment, install R packages and retrieve the data for data analysis.
7. Read the Paper Becker et al., 2022, the data is based on.

Tuesday, July 19

The idea today is to get to know a little the raw data folder and then run the first 3 parts of the R analysis

1. Make sure everything from Monday is completed
2. Look at the raw data folder and its contents

My Part 1 Youtube Video

1. Complete scRNA Workshop Part 1 RMD file.

My Part 2 Youtube Video

1. Complete scRNA Workshop Part 2 RMD file.

My Part 3 Youtube Video

1. Complete scRNA Workshop Part 3 RMD file.

2. Compare what you did today with how things were done in the paper, what can you point out that differs, write these comments in the github discussion page.

Wednesday, July 20

1. Make sure everything from Tuesday is completed
2. Review the Parts 1 through 3

My Part 4 Youtube Video

1. Complete scRNA Workshop Part 3 RMD file.

My Part 5 Youtube Video

1. Complete scRNA Workshop Part 5 RMD file.

Tjursday, July 21

1. Make sure everything from Tuesday is completed
2. Review the Parts 1 through 3

Combined Part 6 and Part 7 Youtube Video

1. Complete scRNA Workshop Part 6 RMD file.

2. Complete scRNA Workshop Part 7 RMD file.

Friday, July 22

Single Cell Raw Data Processing, Youtube Video

1. Review intro to CLI if needed.

2. perform the project setup under data reduction.

3. Read the “Generating Expression Matrix”

4. (OPTIONAL) if you have access to linux and are so inclined generate counts tables using cellrange.