Summer
- Introduction to R
- Introduction to Linux/HPC
- Introduction to NGS (prerequisite: Linux/HPC)
- Introduction to RNA-Seq (prerequisite: R and Linux/HPC)
- Introduction to Metagenomics (prerequisite: R and Linux/HPC)
"Introduction to RNA-Seq" and "Introduction to Metagenomics" 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.
"Introduction to RNA-Seq", "Introduction to NGS" and "Introduction to Metagenomics" workshop days assume knowledge and skills that will be covered in the Introduction to Linux/HPC. Registration for the pre-requisite day is strongly recommended unless the attendee is confident in their abilities or has attended an RIC Introduction to Linux/HPC workshop in the past.
If an attendee opts out of prerequisite 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.
- IN PERSON. Molecular Biology Research Building (MBRB), Rm 1152. NOTE: Light refreshments and lunch will be provided to in-person participants
- ONLINE. NOTE: Details, i.e. URL and access codes, for the online workshop will be provided approximately 1 week before each workshop day.
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. Also, be sure to read our Tips for Online workshops.
If you have any questions please contact us at cribioinfo@uic.edu.
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/mac
Please complete the following items before the workshop days you will be attending.
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/M2/M3 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. Use the link under For older Intel Macs.
- Linux: It is recommended to install via the package management system for your OS. If you have any questions, send an email to cribioinfo@uic.edu.
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.
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.
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/
Remote users will need to use the UIC VPN to access the HPC system (Lakeshore). For instructions on how to setup and use the UIC VPN please visit https://help.uillinois.edu/TDClient/37/uic/KB/ArticleDet?ID=974
Make sure to enable Duo 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.
Setup a SSH client and UIC Duo 2 factor authentication. ONLINE users will also need to setup the UIC VPN. Instructions can be found under Introduction to Linux/HPC
Also 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://igv.org/doc/desktop/#DownloadPage/
NOTE FOR MAC USERS. The "default" installation button for IGV will appear as the Apple chip, a.k.a Apple Silicon. Make sure to install the proper version for your computer. If you computer has an Intel chip be sure to install the Mac Intel version.
If you are not sure if your computer has a Intel or Apple Silicon processor click on the Apple menu and select About this Mac.
In the dialog, if the processor name contains the word "Intel" then it's an Intel chip. If the processor name starts with Apple and has an M number, then it is Apple Silicon.
Setup a SSH client and UIC Duo 2 factor authentication. ONLINE users will also need to setup the UIC VPN. Instructions can be found under Introduction to Linux/HPC
Install R, Rstudio, and Rtools. Instructions can be found under Introduction to R
In addition to the above requirements, install the R packages edgeR, ComplexHeatmap, rtracklayer, ggplot2, and ggrepel 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.
- Install Bioconductor. If you have not already done so, install BiocManager for Bioconductor tools
if ( ! requireNamespace("BiocManager", quietly = TRUE) )
install.packages("BiocManager")- Bioconductor packages. Install edgeR, ComplexHeatmap, and rtracklayer from Bioconductor.
BiocManager::install(c("edgeR", "ComplexHeatmap", "rtracklayer"), update=F)- CRAN packages. Install ggplot2 and ggrepel.
install.packages(c("ggplot2", "ggrepel"))- Check installations. Try to load each package to confirm that the installation was successful:
library(edgeR)
library(ComplexHeatmap)
library(rtracklayer)
library(ggplot2)
library(ggrepel)Setup a SSH client and UIC Duo 2 factor authentication. ONLINE users will also need to setup the UIC VPN. Instructions can be found under Introduction to Linux/HPC
Install R, Rstudio, and Rtools. Instructions can be found under Introduction to R
In addition to the above requirements, also 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 you have not already done so, install BiocManager for Bioconductor tools.
if ( ! requireNamespace("BiocManager", quietly = TRUE) )
install.packages("BiocManager")- Install edgeR, ComplexHeatmap, and biomformat from Bioconductor
BiocManager::install(c("edgeR", "ComplexHeatmap","biomformat"), update=F)- Install vegan from CRAN.
install.packages("vegan")- Check installations. Try to load each package to confirm that the installation was successful:
library(ComplexHeatmap)
library(biomformat)
library(edgeR)
library(vegan)
There are a number of "Take-home" or optional exercises included in the Introduction to Metagenomics workshop. If you wish to run these exercises you will need to install the packages dplyr, tidyr, KEGGREST, ANCOMBC, and mia.
NOTE: Installing these packages is OPTIONAL and not required for the Introduction to Metagenomics workshop.
- Install
dplyrandtidyrfrom CRAN.
install.packages("dplyr")
install.packages("tidyr")- Install
KEGGREST,ANCOMBC, andmiafrom Bioconductor
BiocManager::install(c("KEGGREST", "ANCOMBC", "mia"), update=F)- Check installations. Try to load each package to confirm that the installation was successful:
library(dplyr)
library(tidyr)
library(KEGGREST)
library(ANCOMBC) |
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. |