This report contains the output of cytof analysis.

The aim of this repostiory is to provide code to automatically generate a basic CyTOF analysis report. The intention is for this report to be first executed in whole by using the build report functionality of Rmarkdown. Users can generate their own bespoke project specific code on top of this.

You can find out how to run this report from looking at the help below:

How to run this report

In order to run this report you will need the following input files:

  • One or more design file(s) named design__.csv.
  • A csv file containing the metals expressed in the samples. Called metals_meta_expressed.csv
  • fcs files placed within the directory that the Rmarkdown report will be executed

All input files are reuired to be placed within the directory of the repository before running the report.

In order to begin running the report you will need to double click the cutof_report.Rproj file to open the project. Correctly configure build tools so that the “Build website” button is accessible.

We recommend running the report first without any modifications to the report by pressing Build website. Once the website has rendered the output will be within the docs folder and will look similar to the FlowCore tab.

Next, modify the analysis code to fit your requirements then add additional analysis code and re-run the report.