cytofkit: an integrated mass cytometry data analysis pipeline
NOTE: This is the development version of cytofkit package
cytofkit
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.
Installation
1. Install R and Rstudio
If you have never used R, please install R and Rstudio following the steps below:
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Download the proper R version for your operation system from R download page.
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Double-click the downloaded R installation file, install with all the defaults.
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Download the proper Rstudio version for your operation system from here.
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Double-click the downloaded Rstudio installation file, install with all the defaults.
**Special Notes for Mac Users**
For Mac OS X 10.8 or later, you need to install XQuartz to support the GUI:
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Download the disk image (dmg) file for XQuartz.
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Open the dmg file by double-clicking on it, you’ll find XQuartz.pkg, double-click on it to run the installer, clicking through all the defaults.
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After the installer runs, you’ll have to restart your mac computer.
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
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")
Install this development version, use:
if(!require(devtools)){
install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit")
Usage
After successfully installing the cytofkit package, run the following codes to open the cytofkit GUI:
library("cytofkit")
cytofkit_GUI()
Using the cytofkit shinyAPP to explore your analysis results:
cytofkitShinyAPP()
Check the following vignettes for more details: