Summer - uic-ric/uic-ric.github.io GitHub Wiki
Workshop days
- Thursday, June 15: R
- Friday, June 16: Linux/HPC
- Tuesday, June 20: RNA-Seq (prerequisite: R and Linux/HPC)
- Wednesday, June 21: Next-generation sequencing (NGS) (prerequisite: Linux/HPC)
- Thursday, June 22: Metagenomics (prerequisite: R)
Venue: In-person and Virtual:
- Venue: In-person: Molecular Biology Research Building (MBRB), Rm 1152 (ONLY for people who registered for the In-person workshop)
- Venue - Virtual Online: NOTE: Details, i.e. URL and access codes, for the online workshop will be provided approximately 1 week before each workshop day.
Registration: 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.
If you have any questions please contact us at [email protected].
For details on using reactions, including raising your hand, and the chat in Zoom we recommend viewing the short tutorial video from Zoom titled Zoom In-Meeting Chat and Reactions
- Raising your hand. Click on the "Reactions" icon in the Zoom toolbar at the bottom of the Zoom window. Then click "Raise hand" in the popup dialog. 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 in the "Reactions" popup. 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.
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. This is only a recommended step for online attendees.
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.
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/mac
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].
To update R on Windows, try using the package installr (only for Windows)
1. Open R and install and load installr.
> install.packages("installr")
> library(installr)
2. In R, execute the updateR() function. This will start the updating process of your R installation by: "finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation."
On Mac, you can simply download and install the newest version of R from https://cloud.r-project.org/bin/macosx/. When you restart RStudio, it will use the updated version of R.
Once you have R installed, please install RStudio. The following link has installation instructions and links to the installers for different operating systems.
If you need to update an existing RStudio installation from within RStudio, go to Help > Check for Updates to install newer version of RStudio.
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 (ONLY need 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.
FOR UIC USERS ONLY: Please - make sure to enable 2 factor authentication (2FA) for your account (https://verify.uillinois.edu). Also, make sure to have your chosen 2FA device with you on the workshop days.
NON-UIC USERS: NO ACTION ITEM.
Windows
If you have a Windows computer, you will need to install SSH client prior to the workshop.
- We recommend PuTTY: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
- We recommend WinSCP: https://winscp.net/eng/index.php
If you have a MacOS computer, install an SFTP client.
- We recommend CyberDuck: https://cyberduck.io/
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”, "biomaRt", and "IsoformSwitchAnalyzeR" prior to the workshop day.
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”.
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install(c("edgeR", "ComplexHeatmap","biomaRt","IsoformSwitchAnalyzeR"), update=F)
Try to load each package to confirm that the installation was successful:
library(edgeR) library(ComplexHeatmap) library(biomaRt) library(IsoformSwitchAnalyzeR)
Install the Integrative Genomics Viewer (IGV) prior to the workshop day. The following link has information for installing on macOS, Windows and Linux platforms. Choose the option for your operating system and follow the instructions given on this site.
https://software.broadinstitute.org/software/igv/download
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”, "biomformat" and "vegan" prior to the workshop day.
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”.
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install(c("edgeR", "ComplexHeatmap","biomformat"), update=F)
Install vegan package via CRAN.
If you were asked for a CRAN mirror site, please select one which is close to your location: e.g. “USA (IN)”
install.packages("vegan")
Try to load each package to confirm that the installation was successful:
library(vegan)
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:
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The Research Informatics Core (RIC) provides a broad spectrum of bioinformatics services to the UIC and Chicago-area research communities, including genomics, transcriptomics, epigenomics, metagenomics, metabolomics, and proteomics analysis, as well as applications in statistical analysis, systems biology, and machine learning. |