This page is currently under construction - check back soon!

Software that we may utilise in different workflows (or access ARGUS for a desktop pre-installed with software)

1. Download and install R (latest stable version, or a specific version if needed) from here - https://www.r-project.org/
2. Download and install RStudio Desktop from here - https://www.rstudio.com/products/rstudio/#Desktop
3. Download and install Rtools (for package building from GitHub repositories) - https://cran.r-project.org/bin/windows/Rtools/
4. Download and install devtools (for package building from GitHub repositories - install.packages("devtools")
5. Download and install FlowJo from here (and organise a licence if you haven't already got one)
6. Download and install SeqGeq from here (and organise a licence if you haven't already got one)
7. Download and install Matlab

Excellent links for information that was used for R/Rstudio/flowCore

1. Basic intro to R - https://cran.r-project.org/doc/contrib/Torfs+Brauer-Short-R-Intro.pdf
2. Introduction to flowCore - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-106
3. R package vigenettes (which are the mini guides for each package developed in R)

Data pre-processing in FlowJo using R plugins

FlowJo check sample quality

In FlowJo, after importing your cytometry data, click the 'Check sample quality' button in the tools workspace. This will flag samples that should be checked. FlowJo plots the median values for each parameter over time and flags any that are outside of 2 standard deviations. Green is good. Any thing else should be reviewed. 

Active sample quality check - FlowAI in FlowJo

FlowJo also provides access to 2 active cytometry data quality plugins. FlowClean & FlowAI

To enable FlowAI

• Have R installed (version >3.4)
• Install BioConductor & flowCore
  • source("https://bioconductor.org/biocLite.R")
  • biocLite()
  • biocLite("flowCore")
• Install PNG package
  • install.packages("png")
• Install flowAI
  • biocLite("flowAI")
• Install stringi (I required this package additionally)
  • biocLite("stringi")
• Load libraries in R
  • library(flowCore)
    library(stringi)
    library(flowAI)
• Have FlowJo installed with the correct R path in the preferences
  
• If not already present, download and move FlowAI.jar file into the FlowJo plugins folder (available from the FlowJo exchange)
• Restart FlowJo
• Select sample and navigate to Plugins, FlowAI. Select parameters and compute. Example output is shown below including layout depiction.
  
  

Active sample quality check - FlowClean in FlowJo

To enable FlowClean

• Have R installed (version >3.4)
• Install BioConductor
  • source("https://bioconductor.org/biocLite.R")
  • biocLite("flowCore")
  • biocLite("flowClean")
• Load libraries in R
  • library(flowCore)
    library(flowClean)
• Have FlowJo installed with the correct R path in the preferences
  
• If not already present, download and move FlowClean.jar file into the FlowJo plugins folder (available from the FlowJo exchange)
• Restart FlowJo
• Select sample and navigate to Plugins, FlowClean. Select parameters and compute. Example output is shown below.
  

Reading and analysing FCS files in R/RStudio

Please note I am no expert in R/RStudio and apologise in advance if my nomenclature or the below has errors.This is still under construction so please email me and we can update this guide ASAP.

1. Open RStudio (ensure you run as administrator, otherwise you may run into permission errors).
2. Make a new project (a project can be considered a workspace where everything can be saved to)

3. Some basic packages/libraries should be installed while working with flow data, this list isn't comprehensive but it contains some useful basics. 

   source("https://bioconductor.org/biocLite.R")
   biocLite()
   biocLite("FlowSOM",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("flowCore",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("flowViz",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("flowUtils",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("geneplotter",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("Seurat",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("stringi",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("yaml",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("dplyr",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("openCyto",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("tsne",dependencies=TRUE,suppressUpdates=TRUE)
   biocLite("Rtsne",dependencies=TRUE,suppressUpdates=TRUE)
   
   install.packages("dplyr",dependencies=TRUE,suppressUpdates=TRUE)
   install.packages("yaml",dependencies=TRUE,suppressUpdates=TRUE) 
   install.packages("devtools",dependencies=TRUE,suppressUpdates=TRUE)
   
   library(flowCore)
   library(FlowSOM)
   library(flowViz)
   library(flowUtils)
   library(geneplotter)
   library(Seurat)
   library(dplyr)
   library(yaml)
   library(stringi)
   library(openCyto)
   library(tsne)
   library(Rtsne)

   Note: There are many Vignettes in the packages which are ever so helpful. Vignettes are help guides that can help to show you how to use different tools/functions.
   
   

4. Some commonly used codes - good to get familiar with

   #gets to working directory
   getwd()
   #sets the working directory
   setwd('C:/Users/utopi/Desktop/testdata')
   #assign a file to a variable
   fileName <- "C:/Users/utopi/Desktop/testdata/sample.fcs"
   #assign a folder to a variable
   folderName <- "C:/Users/utopi/Desktop/testdata/"
   #read a FCS file to a variable using read.FCS from flowCore
   data1 = read.FCS('A1.fcs')
   #assign a variable an example data file i.e. from a vignette example
   fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")

5. Workflow to try
   flowClust workflow in vignette
   flowSOM workflow in vignette 
   openCyto workflow in vignette
6. Lets analyse some data..
7. Put your data in a folder on your computer
8. In RStudio go to file and then new R script (we will be writing the script so that we can rerun it if needed)
9. Lets assign the folder to a variable