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George Chlipala edited this page Feb 29, 2024 · 15 revisions

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General Information

Workshop days

  1. Introduction to R
  2. Advanced Topics in R
  3. Advanced Statistics in edgeR
  4. Single Cell RNA-seq
  5. Pathway Analysis

Prerequisites

"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 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.

Venue(s)

  • IN PERSON. Molecular Biology Research Building (MBRB) at 900 S. Ashland Ave., Rm 1009. NOTE: Light refreshments and lunch will be provided to in-person participants. Note for non-UIC registrants: The closest public parking lot is the Paulina street garage, 915 S Paulina. The Pink line Polk stop is also nearby.

  • ONLINE. 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. Also, be sure to read our Tips for Online workshops.

If you have any questions please contact us at cribioinfo@uic.edu.

Desktop/Laptop Requirements

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

External display (OPTIONAL and ONLINE Users ONLY)

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.

Things to install prior to the workshop

Please complete the following items before the workshop days you will be attending.

Introduction to R

Install R on your laptop

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.

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

Install RStudio

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

Install Rtools

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.

XQuartz (Mac users only)

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

Advanced Topics in R

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 "openxlsx" 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('openxlsx')

After installation, try to load each package to confirm that the installation was successful.

library(ggplot2)
library(doBy)
library(reshape2)
library(readxl)
library(openxlsx)

Advanced Statistics in edgeR

Install R, Rstudio, and Rtools. Instructions 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.

  1. CRAN packages
install.packages('ggplot2')
  1. Install Bioconductor. If you have not already done so, install BiocManager for Bioconductor tools
if ( ! requireNamespace("BiocManager", quietly = TRUE) ) 
  install.packages("BiocManager")
  1. Bioconductor packages. 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)
  1. Check installations. Try to load each package to confirm that the installation was successful:
library(edgeR)
library(ComplexHeatmap)
library(circlize)
library(biomaRt)
library(ggplot2)

Single Cell RNA-seq

Install R, Rstudio, and Rtools. Instructions 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.

  1. If you have not already done so, install BiocManager for Bioconductor tools
if ( ! requireNamespace("BiocManager", quietly = TRUE) ) 
  install.packages("BiocManager")
  1. Seurat. Seurat requires the multtest package from Bioconductor, but it is installed from CRAN:
BiocManager::install('multtest', update=F) 
install.packages('Seurat')
  1. Install Matrix, dplyr, and fossil from CRAN
 install.packages('Matrix')
 install.packages('dplyr')
 install.packages('fossil')
 install.packages('ggplot2')
  1. Install ComplexHeatmap and monocle from Bioconductor
BiocManager::install("ComplexHeatmap", update=F)
BiocManager::install("monocle", update=F)
  1. Install CytoTRACE, which is from a custom repository. This is optional, but we include a take-home exercise using CytoTRACE if you would like to try it:
  • Download the CytoTRACE installation source from https://cytotrace.stanford.edu/. For the latest version go to the CytoTRACE website and then click on Install R Package in the sidebar menu.
  • Execute the following commands in R. Modify the PATH/TO/DOWNLOAD to reflect the directory where you download the CytoTRACE installation package. You may need to install the devtools R package also.
if ( ! requireNamespace("devtools"))
   install.packages("devtools")

devtools::install_local("PATH/TO/DOWNLOAD/CytoTRACE_0.3.3.tar.gz")

NOTE: If CytoTRACE could not be installed because ERROR: dependency 'sva' is not available for package 'CytoTRACE', install “sva” using BiocManager.

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

Note that when you load the CytoTRACE library there may be additional warnings that Python packages scanoramaCT and numpy are required for analyzing across multiple batches. For our purposes we do not need this functionality and these warnings can be ignored. Refer to the CytoTRACE documentation for more details (https://cytotrace.stanford.edu/).

  1. 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)
library(CytoTRACE)

Pathway Analysis

Install R, RStudio, Rtools and important R packages

Install R, Rstudio, and Rtools. Instructions 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.

  1. If you have not already done so, install BiocManager for Bioconductor tools
if ( ! requireNamespace("BiocManager", quietly = TRUE) ) 
  install.packages("BiocManager")
  1. Install ggplot2, circlize and reshape2 from CRAN.
install.packages('ggplot2')
install.packages('circlize')
install.packages('reshape2')
  1. Install ComplexHeatmapfrom Bioconductor:
BiocManager::install("ComplexHeatmap", update=F)
  1. Try to load each package to confirm that the installation was successful:
library(ggplot2)
library(circlize)
library(reshape2)
library(ComplexHeatmap)

GenePattern registration

  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.

MSigDB registration

  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

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.

https://rrc.uic.edu/cores/research-informatics-core/

Workshop general details

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