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Workflows
| Algorithm | Visually | Identification | Example output | ||
|---|---|---|---|---|---|
| Data pre-processing | |||||
| Novel population discovery | |||||
| What is different and of interest? | |||||
| Time course | |||||
| Alignment of data | |||||
| Single cell RNA sequencing |
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- Download and install R (latest stable version, or a specific version if needed) from here - https://www.r-project.org/
- Download and install RStudio Desktop from here - https://www.rstudio.com/products/rstudio/#Desktop
- Download and install FlowJo from here (and organise a licence if you haven't already got one)
- Download and install SeqGeq from here (and organise a licence if you haven't already got one)
- Download and install Matlab
Data pre-processing
FlowJo Check Sample Quality
In FlowJo, after importing your cytometry data, click the 'Check sample quality' button in the tools work space. This will identify any 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.
FlowJo Active Check Sample Quality Plugin Access
FlowJo also provides access to 2 active cytometry data quality plugins. FlowClean and AIClean. Before you use these you must do this:& FlowAI
To enable FlowAI
- Have R installed (version >3.4)
- Install flowCore (copy and paste the following)
- source("https://bioconductor.org/biocLite.R")
- biocLite("flowCore")
- Install PNG package
- install.packages("png")a
- Install flowAI
- source("https://bioconductor.org/biocLite.R")
- biocLite("flowAI")
- Have FlowJo installed with the correct R path in the preferences
- Download and locate FlowAI.jar file into the FlowJo plugins folder.
- Restart FlowJo
- Select sample and navigate to Plugins, FlowAI.
These can be accessed from the plugins menu.
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