Table of Contents General Information General guidelines for using_Zoom Tips for using Zoom Desktop/Laptop Requirements External display Things to install prior to the workshop Introduction to R Install R on your laptop Install RStudio Install Rtools XQuartz (Mac users only) Advanced Topics in R CRAN packages Check installations Advanced Statistics in edgeR CRAN packages Bioconductor Bioconductor packages Check installations Single Cell RNA-seq Bioconductor Seurat CRAN packages Bioconductor packages Check installations Pathway Analysis Bioconductor CRAN packages Bioconductor packages Check installations GenePattern registration MSigDB registration Helpful Resources Cheatsheets Tutorials

Workshop days

1. Wed Feb 08: Introduction to R
2. Wed Feb 15: Advanced Topics in R
3. Tues Feb 23: Advanced Statistics in edgeR
4. Wed Mar 01: Single Cell RNA-seq
5. Wed Mar 08: Pathway Analysis

Pre-requisite: "Advanced Topics in R", "Advanced Statistics in edgeR", "Advanced Statistics in edgeR", "Single Cell RNA-seq" and "Pathway Analysis" workshop days assume knowledge and skills that will be covered in the Introduction to R workshop. Registration for the pre-requisite day is strongly recommended unless the attendee is confident in their abilities, or has attended an RIC Introduction to R workshop in the past. If an attendee opts out of pre-requisite workshop day(s), they assume full responsibility for the level of skill required for the later workshop days. No refunds, discounts, or supplementary lessons will be given.

Venue: INPERSON. Molecular Biology Research Building (MBRB), Rm 1009. NOTE: Light refreshments and lunch will be provided to in-person participants

Venue: ONLINE. NOTE: Details, i.e. URL and access codes, for the online workshop will be provided approximately 1 week before each workshop day.

Food: Light refreshments and lunch will be provided to in-person participants. We recommended coming in at least 15 minutes early. Refreshments will be served starting 8.30 AM. No food and drinks are allowed in the instruction room - so please come early.

Time: Sessions begin promptly at 9 am and end at 4:45 pm.

Zoom Registration: For ONLINE participants only. You will have to register for each workshop separately. Zoom registration details will be sent to all the attendees prior to the workshop.

If you have any questions please contact us at [email protected].

On the day of the workshop, all members of the Research Informatics Core will be logged-in as co-hosts for the Zoom event and any one of us will be available to answer questions or provide assistance during the exercises. The members of RIC will be in communication with each other during the entirety of the workshop and will be able to coordinate assistance to any attendees in need.

To gain attention of the co-hosts or presenter the Zoom application has the capability for an attendee to "raise their hand" or ask a question. The attached "Tips for using Zoom" has information on how to "raise your hand" or ask a question. For this workshop we would ask that the attendees use these features as follows.

• If you need assistance during one of the exercises, we ask that you use the “raise your hand” feature of Zoom. A member of RIC will contact you via the chat feature that is part of the Zoom event.
  • Please do NOT try to contact a RIC member via chat or directly enter a breakout session as they may be assisting another attendee while a different RIC member may be available to provide assistance.
  • If needed, the RIC member will create a breakout session during the Zoom meeting for you and a member of RIC to allow for screen sharing. Once assistance has been provided and you no longer require help, please exit the breakout room return to the main Zoom event for the workshop. If you require additional assistance at a later time, please use the “raise your hand” feature again.
• If you have a question during the lecture or exercise portions of the workshop, please use the “Chat” feature of Zoom. Please send all questions to “Everyone”, so any available co-host would be able to answer the question.

In further preparation for the online workshop, please download and install the Zoom application prior to Thursday. This will streamline connecting to the Zoom Event.

• https://zoom.us/support/download

If you already have Zoom installed on your computer, be sure to update Zoom prior to Wednesday, July 28th. To update the Zoom application, open the application and then click on the icon for your user profile (this would have your initials). In the menu that appears, select “Check for Updates”. Follow the dialogs to update your Zoom application, if an update is needed.

If you have any questions please contact us at [email protected].

• Raising your hand. Click on the “Raise Hand” button near the bottom of the “Participants” window. Once a panelist has responded to you please “lower your hand” by clicking on the Lower button

After you have “raised your hand” be sure to open the Chat panel as a panelist will likely contact you via chat.

• Providing Feedback. If you find that the pace of instruction is to too fast or too slow, you can use the feedback buttons on the bottom of the participants window. Use “go slower” if you think the pace is too fast and use “go faster” if you think the pace of instruction is too slow.

Laptop/desktop computer with at least 4GB RAM. Windows, Mac, or Linux, and high-speed Internet connection.

If you have access to an external display, we recommend that you setup your laptop with an external display and extend your desktop so that you can have separate screens for the online workshop and your work, i.e. RStudio or SSH client. Please note. If you do NOT have an external display, you will still be able to fully participate in the workshop. Having an external display is NOT a requirement for the workshop. The following URLs have instructions for setting up a dual display for different operating systems.

• Window 10: https://support.microsoft.com/en-us/help/4340331/windows-10-set-up-dual-monitors
• Windows 7: https://support.microsoft.com/en-us/help/976064/guided-help-dual-monitor-setup-is-easy-in-windows-7
• macOS: https://support.apple.com/guide/mac-help/use-multiple-displays-mchl7c7ebe08/m​ac

The following are links to installation instructions for R. We will be using v4 for the workshop. Please use the link that corresponds to the operating system on your laptop.

• Windows: https://cran.rstudio.com/bin/windows/base/
• MacOS: https://cran.rstudio.com/bin/macosx/
  • Note for Mac M1 users: we still recommend installing the Intel build of R, which will run fine through Rosetta. You will likely have more success installing packages with this build.
• Linux: It is recommended to install via the package management system for your OS. If you have any questions, send an email to [email protected].

If you have an older version of R installed on your laptop please update to v4. Instructions on updating R can be found at https://uic-ric.github.io/workshop/updateR.html

Once you have R installed, please install RStudio. The following link has installation instructions and links to the installers for different operating systems.

• Rstudio: https://www.rstudio.com/products/rstudio/download/#download

This is a set of tools that allows R to compile certain packages. Please use the link that corresponds to the operating system on your laptop.

• Windows: https://cran.rstudio.com/bin/windows/Rtools/
• macOS (install Xcode and GNU Fortran compiler): https://mac.r-project.org/tools/

This installs the XQuartz terminal for Mac, which is a necessary external dependency for Cairo, which in turn is used by the ComplexHeatmap package to draw heatmaps.

https://www.xquartz.org

Install R, Rstudio, Rtools, instruction can be found under "Introduction to R".

In addition to the above requirements, we also recommend that you install the R packages "ggplot2", "doBy", "reshape2", "readxl", and "xlsx") prior to the workshop day. If you have already installed these packages, there is no need to install them again.

To install these packages, open an RStudio session and in the Console window, in the bottom left of RStudio, type the following commands. If the installation process asks you to “Update all/some/none [a/s/n]:” respond with “n”.

 install.packages('ggplot2')
 install.packages('doBy')
 install.packages('reshape2')
 install.packages('readxl')
 install.packages('xlsx')

Try to load each package to confirm that the installation was successful:

  library(ggplot2)
  library(doBy)
  library(reshape2)
  library(readxl)
  library(xlsx)

Install R, Rstudio, Rtools, instruction can be found under "Introduction to R".

In addition to the above requirements, we also recommend that you install the R packages “edgeR”, “ComplexHeatmap”, "circlize", "biomaRt", and "ggplot2" prior to the workshop day. If you have already installed these packages, there is no need to install them again.

To install these packages, open an RStudio session and in the Console window, in the bottom left of RStudio, type the following commands. If the installation process asks you to “Update all/some/none [a/s/n]:” respond with “n”.

 install.packages('ggplot2')

If you have not already done so, install BiocManager for Bioconductor tools:

  if (!requireNamespace("BiocManager", quietly = TRUE)) 
      install.packages("BiocManager")

Install edgeR, ComplexHeatmap and biomartRT from Bioconductor:

  BiocManager::install("edgeR", update=F)
  BiocManager::install("ComplexHeatmap", update=F)
  BiocManager::install("circlize", update=F)
  BiocManager::install("biomaRt", update=F)

Try to load each package to confirm that the installation was successful:

  library(edgeR)
  library(ComplexHeatmap)
  library(circlize)
  library(biomaRt)
  library(ggplot2)

Install R, Rstudio, Rtools, instruction can be found under "Introduction to R".

In addition to the above requirements, we also recommend that you install the following R packages: "Seurat", "Matrix", "dplyr", "fossil", "ComplexHeatmap", "ggplot2", and "monocle". If you have already installed these packages, there is no need to install them again.

If you have not already done so, install BiocManager for Bioconductor tools:

 if (!requireNamespace("BiocManager", quietly = TRUE)) 
     install.packages("BiocManager")

Seurat requires the multtest package from Bioconductor, but it is installed from CRAN:

 BiocManager::install('multtest', update=F) 
 install.packages('Seurat')

Install Matrix, dplyr, and fossil from CRAN:

 install.packages('Matrix')
 install.packages('dplyr')
 install.packages('fossil')
 install.packages('ggplot2')

Install ComplexHeatmap and monocle from Bioconductor:

  BiocManager::install("ComplexHeatmap", update=F)
  BiocManager::install("monocle", update=F)

Try to load each package to confirm that the installation was successful:

  library(Seurat)
  library(Matrix)
  library(dplyr)
  library(fossil)
  library(ComplexHeatmap)
  library(monocle)
  library(ggplot2)

Install R, Rstudio, Rtools, instruction can be found under "Introduction to R".

In addition to the above requirements, we also recommend that you install the following R packages: "ggplot2", "circlize", "reshape2", and "ComplexHeatmap". If you have already installed these packages, there is no need to install them again.

If you have not already done so, install BiocManager for Bioconductor tools:

 if (!requireNamespace("BiocManager", quietly = TRUE)) 
     install.packages("BiocManager")

 Install ggplot2, circlize and reshape2 from CRAN:
 install.packages('ggplot2')
 install.packages('circlize')
 install.packages('reshape2')

Install ComplexHeatmapfrom Bioconductor:

  BiocManager::install("ComplexHeatmap", update=F)

Try to load each package to confirm that the installation was successful:

  library(ggplot2)
  library(circlize)
  library(reshape2)
  library(ComplexHeatmap)

1. Open a web browser and navigate to https://cloud.genepattern.org/gp/pages/registerUser.jsf
2. Fill out the registration form
   • Enter a username that you will use to login
   • Create a password for your account
   • Fill in your email address
   • You can unselect Add me to the GenePattern users mailing list to opt-out of the email list.
   • Click “I’m not a robot”
3. Click Create My Account

The GenePattern will then create your account and will open the GenePattern web application. There is not additional steps you need to take and you can close your web browser.

1. Open a web browser and navigate to https://www.gsea-msigdb.org/gsea/register.jsp
2. Fill out the registration form
   • Fill in your email address
   • Enter your organization, e.g. “University of Illinois at Chicago” or “University of Chicago”
3. Click Register

We have also gathered a number of cheat-sheets that will be useful for many of our different workshops. These cheat-sheets are available at

https://uofi.box.com/v/ricworkshops-cheatsheets

We have also prepared tutorial videos describing, e.g., using SFTP clients to download data from a server. These may be useful to review prior to the workshops, in particular the Linux/HPC day, and may serve as a reference after the workshops as well. You can find a listing of these tutorials here:

Tutorials