==Citrus Readme== Citrus is a package for identifying clusters of cells in multidimensional flow cytometry data associated with an experimental or clincal endpoint of interest. Methods are described in the paper [[https://doi.org/10.1073/pnas.1408792111|Automated identification of stratifying signatures in cellular subpopulations]] by Bruggner et al.

===Getting Started===

• Installation instructions available on the [[https://github.com/nolanlab/citrus/wiki/Installing-Citrus|Installing Citrus Page]].
• Instructionson how to configure Citrus for your data available on the [[https://github.com/nolanlab/citrus/wiki/Getting-Started|Getting Started]] Page.
• Example analyses available on the [[https://github.com/nolanlab/citrus/wiki/Examples|Examples Page]].
• See the [[https://github.com/nolanlab/citrus/wiki/Citrus-FAQ|Citrus FAQ]] for questions related to building and/or running Citrus. ===Version History=== ;Version 0.08 : - Completely refactored codebase that is hopefully much more intuitive. : - Documentation added. ;Version 0.07 : - Multiclass analysis available for SAM and Nearest Shrunken Centroid models : - Small GUI enhancements ;Version 0.06 : - Changed feature names : - Many new graphical outputs for result visualization ;Version 0.05 : - Adding support for SAM (two-class only) ;Version 0.04 : - Adding support for Survival analysis (glmnet model only) ;Version 0.03 : - Switching to ggplot2 and adding feature heiarachy plots ;Version 0.02 : - Now includes shiny web GUI for running citrus ;Version 0.01 : - Initial Citrus Test Code