i-cyto

Atelier AFC 2020

The commands are glued in a R Markdown script. We propose a RECAP of the classical pipelines. To redo the R session, please follow the PRESENTATION.

You can simplify the selecion of markers by using a text file of the markers to analyze. Just type this file name into the marker selection field.

Then it’s possible to continue the analysis with cytofast. Here is the html resulting from the data exported from cytofkit. You need to define sample groups in a meta.csv file. Then you get nice heatmaps, compute t-test of percentages and Volcano plots.

Installation commands

• Please do copy/paste commands line by line
• Whenever you get a message ‘Update all/some/none? [a/s/n]:’, answer n
• If you get a dialog box asking to install from source, answer no

  if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
  BiocManager::install("flowCore")
  BiocManager::install("uwot")
  BiocManager::install("cytofast")
  

  # install devtools if not already done
  if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
  # install Rphenograph if not already installed
  if (!requireNamespace("Rphenograph", quietly = TRUE))
    devtools::install_github("i-cyto/Rphenograph")
  # install cytofkitlab
  devtools::install_github("i-cyto/cytofkitlab")
  

Updates

• v1 2020-02-05: html result from script