Intro to Single Cell RNA-Seq Workshop

Wrapping up

We hope you now have more familiarity with key concepts, data types, tools, and how they all connect to enable single-cell gene expression analysis from RNA-Seq data.

Wayfinder: Wrap-up

Housekeeping

Please take our optional post-workshop survey (5-10 minutes).
We will email you a link to the final session recordings next week.
The website/notes for this workshop will be available.
The UM Bioinformatics Core Workshop Slack channel content will be available for 90 days.

Can I continue to use the RStudio environments we used in the workshop?

The RStudio workshop compute environment will be available through 8/15/2025.
- Please save all your R scripts now so that we can “right-size” the compute environment immediately following today’s workshop session.
You can download files from the workshop environment from your terminal/command line window as below. (You will need to substitute your actual workshop username and type workshop password when prompted.)
```
# download workshop files -------------------------------------------------
mkdir intro_scrnaseq_workshop
cd intro_scrnaseq_workshop
scp -r YOUR_USERNAME@bfx-workshop01.med.umich.edu:"ISC_R*" .
```
- Note that the full download of the R data is about 8Gb, so depending on your internet speeds it could take a while. (We do not recommend you download the full set of Cell Ranger outputs.)

Where else could I use RStudio?

See Advanced setup instructions for details on how to install RStudio and required packages on your own computer. Please note:
- Installing bioinformatics software is often non-trivial.
- For typical data, Cell Ranger steps (reviewed Day 1) assume your computer has powerful compute (many CPUs and lots of RAM) and sizable storage capacity. (i.e. it’s impractical to run these on your laptop.)
PositCloud allows you to run R-Studio over the web for free. Click here to login to PositCloud and launch an R session. (UM users can login using their umich.edu Google account.) Note: A full single-cell analysis will require you to upgrade beyond the free tier.
UMich users can run RStudio on the UM Great Lakes HPC.

Could I download Seurat inputs used in the workshop?

The Seurat inputs (cellranger triples and dbcells files) used in this workshop can be installed locally like so:

# download Seurat inputs --------------------------------------------------
mkdir -p intro_scrnaseq_workshop/ISC_R
cd intro_scrnaseq_workshop/ISC_R

# Use curl to download a ~3 Gb tarball
# We'll use evironment variables to avoid extremely long command lines
source_url="https://umich-brcf-bioinf-workshop.s3.us-east-1.amazonaws.com"
source_file="ISC/workshop_isc_inputs-20250730.tgz"
curl -o workshop_isc_inputs.tgz ${source_url}/${source_file}

# tar unpacks the tarball into directories
tar xzvf workshop_isc_inputs.tgz

# Since we have unpacked the tarball, we can remove it
rm workshop_isc_inputs.tgz