Workshop goals and topics

  • By the end of the workshop, attendees will be able to

    • Describe (at a high level) how sc samples are sequenced along with strengths of a few popular library preps.
    • Create and interpret preliminary QC visualizations from a sc experiment.
    • Use Seurat, PCA, and UMAP to create cell-type clusters and projections.
    • Identify marker genes and annotate clusters based on gene expression.
    • Execute and visualize differential expression across clusters.

  • This workshop is targeted toward researchers who would like to be able to run scRNA-Seq analysis independently. This workshop assumes some experience working with R/R-Studio. Basic understanding of NGS sequencing protocols and/or familiarity with bulk RNA-Seq analysis is desirable.

  • Please let us know if there is anything we can do to improve the workshop experience.

  • Our purpose is not to be exhaustive, there is a lot that we cannot cover in the allotted time, and we don’t expect anyone to be an expert at the end of the workshop. But we hope you will have a familiarity with key concepts, data types, tools, and how they all connect to one another in the service of a biological question.

About the workshop team
Chris Marci Raymond Dana
Travis Olivia Ram
Matt Joe Nick


Code of Conduct

  • Be kind to others. Do not insult or put down others. Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate for the workshop.

  • All communication should be appropriate for a professional audience including people of many different backgrounds. Sexual language and imagery is not appropriate.

  • The Bioinformatics Core is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion. We do not tolerate harassment of participants in any form.

  • Thank you for helping make this a welcoming, friendly community for all.

  • If you have questions about the CoC please reach out to the hosts during the workshop, or email us at .

  • To report a CoC incident/concern, please email Chris Gates (Bioinformatics Core, Managing Director) at or contact the University of Michigan Office of Institutional Equity at .

Using Zoom and Slack

  • We will be recording this session. Recordings will be available to participants
    following the workshop.

Zoom

  • Zoom controls are at the bottom of the Zoom window: Zoom controls

  • To minimize distractions, we encourage participants to keep their audio muted (unless actively asking a question).

  • To maximize engagement, we encourage participants to keep their video on.

  • Slack works better than Zoom’s Chat function so avoid Zoom Chat for now.

  • You can enable transcription subtitles for your view.

  • We will be using Breakout Rooms occasionally for ad-hoc 1-1 helper support. We will review this in detail together in a few minutes.

  • Zoom’s “Reactions” are a useful way to interact. You can access these from the React button. Zoom non verbals

    • Raise Hand to request clarification or ask a question. (Same an in-person workshop.)
    • Instructors will use Green check and Red X to poll the group at checkpoints along the way.

Exercise: Use Zoom non-verbals

  • Everyone use Zoom to raise your hand.

Exercise: Using Zoom Breakout Rooms

Take a moment to briefly introduce yourself (name, dept/lab, area of study) in a breakout room.

  • Zoom: Click Breakout Rooms
  • Find the room corresponding to the first letter of your first name
  • Click Join button to the right of the room.
  • When you have completed introductions, you can leave the breakout room to rejoin the main room.

Breakout rooms

Slack

  • Slack can be used to communicate to the group or to individuals and has a few features/behaviors that we prefer over Zoom’s Chat functionality.
Posting messages to Slack
Posting messages to Slack
  • Slack messages will be posted to the 2024-02-intro-single-cell channel.
    Click on the channel in the left pane (1) to select this channel.
  • You can type in the message field (2); click send (3) to post your message to everyone.
  • Helpers will respond in a Slack thread (or pose the question to the instructor)
  • You can respond in a message thread by hovering over a message to trigger the message menu and clicking the speech bubble (4).

Exercise: Responding in Slack thread

In your scRNA-Seq experiment, what do/did you hope to find?

Review of Key communication patterns

Zoom Slack
“I have an urgent question” Post a question
“I have a general question” Post a question
“I’m stuck / I need a hand” Post a note
Instructor check-in -or-
Instructor Slack question Respond in Slack thread



Exercise: Group checkpoint

  • Using Zoom, give me a green-check if you feel like you understand communication patterns or red-X if you need clarification.

Logging in to the shared server

To start, we will access our shared RStudio server by opening a web browser to the following URL:

(The correct URL will be supplied by the instructor via Slack.)

You should now be looking at a page that will allow you to login to the RStudio server:

Image: Login page for RStudio server.
Image: Login page for RStudio server.

Enter your user credentials and click Sign In. Your username and password were provided via email, but if you need help, a helper can retrieve it for you if you ask in Slack.

Once you click Sign In, your screen will go blank for a few seconds. This sometimes will feel like a longer delay (possibly up to 60 seconds); this is ok.

Once logged in, you should now see the RStudio interface:

Image: Landing page after successful login to RStudio server.

Arranging your screens

It is important that you can see:

  • Zoom (instructor’s shared screen + reactions)
  • Your R/Studio screen
  • Slack
  • Lesson plan web page

arranged screens

Any questions?

Thank you to our sponsors/contributors

UM BRCF Bioinformatics Core

  • The University of Michigan BRCF Bioinformatics Core is a team of analysts that help researchers design, analyze, and interpret high-throughput genomics experiments.
  • Last year we helped about 60 researchers design and execute about 100 projects including gene expression, epigenetic, variant identification, functional enrichment and many other kinds of analyses.
  • We provide letters of support for grant proposals.
  • We are creating a series of bioinformatics-focused workshops.

Biomedical Research Core Facilities

Biomedical Research Core Facilities (BRCF) helps researchers economically take advantage of the latest technology and collaborate with top experts in the field. Established in 1986, the BRCF was formed to offer centralized access to research services and equipment.

University of Michigan Library

Our mission is to support, enhance, and collaborate in the instructional, research, and service activities of faculty, students, and staff, and contribute to the common good by collecting, organizing, preserving, communicating, sharing, and creating the record of human knowledge.



Acknowledgements