X-Cyt Manual (v1.0)

X-Cyt follows user-selected scheme and template to partition cytometric data.
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Software and Packages

1. Download and install R (v3.0.0 or later) for your platform HERE .
2. Download X-Cyt R package HERE . Note the download destination folder, but do not need to unzip.
3. Download EMMIX-skew R package for your platform. Do not need to unzip.

Install R Packages

1. In R, go to "Packages & Data" tab, click on "Package Installer". From the first pull down menu (default is "CRAN (binaries)"), select "Local source package" then click "Install". Locate "xcyt_1.0.tar.gz" and click "Open". This will install the X-Cyt R package.
2. Repeat package installation for EMMIX-skew.
3. To load EMMIX-skew and X-Cyt into R in a current session, type in the R console: require(emmixskew), and require(xcyt).

Sample Data Analysis

We recommend running the iNKT dataset on a Unix server, as each data file contains more than 2.5 million events.

1. Download either the CD4 T cell or iNKT cell sample dataset HERE . Unzip all data sample files (.txt) into a folder.
2. Download sample user-input files HERE . Unzip to a folder (contains both EMT and NKT subfolders).
3. Download the R script for analyzing the sample datasets HERE .