Commmand Line Tools
OpenCytoCL command line tools under development.
The OpenCyto paper is has been published here.
The appropriate citation is:
Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R. OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis. PLoS Comput Biol. 2014 Aug 28;10(8)
PubMed PMID: 25167361; PubMed Central PMCID: PMC4148203.
The latest version of OpenCyto contains some changes to the way templates are written for
tailgate gates. We have moved the preprocessing for
tailgate to be explicit. The
collapseDataForGating should be set to
FALSE and the
preprocessing_method should be set to
standardize_flowset, in order to get the same behavior as previously by default when
collapseDataForGating was set to
A good place to start is the package vignette.
More information on integrating your own gating functions is here
This is work in progress. Existing gating functions are documented here
SDY207 (CyTOF data)
HVTN080 (HIV Vaccine Clinical Trial Data)
Did you find a bug?
Please file a bug report! We count on you to let us know if something isn’t working as expected. Your feedback makes the software better for everyone.