cytofkit: an integrated mass cytometry data analysis pipeline

NOTE: This is the development version of cytofkit package


This package is designed to facilitate the analysis workflow of mass cytometry data with automatic subset identification and mapping of cellular progression. Both command line and a GUI client are provided for executing the workflow easily.


1. Install R and Rstudio

If you have never used R, please install R and Rstudio following the steps below:

Special Notes for Mac Users

For Mac OS X 10.8 or later, you need to install XQuartz to support the GUI:

2. Install cytofkit package

The offical and stable version, please refer to

Install the stable version from Bioconductor, use:

## try http:// if https:// URLs are not supported

Install this development version, use:

  install.packages("devtools") # If not already installed


After successfully installing the cytofkit package, run the following codes to open the cytofkit GUI:


Using the cytofkit shinyAPP to explore your analysis results:


Check the following vignettes for more details:

Try the cytofkit package in your browser

Any scripts or data that you put into this service are public.

cytofkit documentation built on Nov. 1, 2018, 3:50 a.m.