cnicholasmda / cyt3

Matlab GUI for analysis of mass cytometry data

cyt3

Setup:

Clone the cyt3 repository using $> git clone git://github.com/dpeerlab/cyt3.git

In Matlab, go to 'file>set path...>Add with Subfolders' select the directory where cyt3 was cloned. click 'Save' click 'Close'

Launch: Type 'cyt' in the matlab command line.

FAQ

1. when I launch SightOf, Matlab complains about not finding files. did you add sightof (with subfolders!) to your path as described in the setup section? if not, please do so and don't forget to save. If yes, please contact support with the error.

2. How do I load my data? Sight, accepts new data in FCS format. any piece of data is considered a gate. To load new data, click on the green '+' button in the gates panel.

A tutorial on using cyt can be found here: https://github.com/dpeerlab/cyt3/blob/master/cyTutorial.ppt. Tutorial for running meta clustering is here: https://github.com/dpeerlab/cyt3/blob/master/Meta%20Clustering.pptx.

Python versions for some of the tools within cyt

1. Phenograph: https://github.com/dpeerlab/PhenoGraph
2. Wanderlust/Wishbone: https://github.com/dpeerlab/wishbone