Extract and Analyze Median Molecule Intensity from 'citrus' Output
Gets matrices of medians for each individual sample for all measured p...
Gets matrices of medians for each individual sample for all measured p...
Gets matrix of medians for desired measured features for all clusters ...
Plot dot plots of features where both clusters are significantly diffe...
Plot dot plots of features where one cluster is significantly differen...
Filters list of data matrices with columns corresponding to the measur...
Filters list to contain only desired clusters
Assesses significance of ANOVA and t-test results
Plot dot plots of features where both clusters are significantly diffe...
Plot dot plots of features where one cluster is significantly differen...
Runs ANOVA and t-tests comparing clusters and markers in clusters
Processes cluster signaling data in form for statistical analysis
Reorders to rows (corresponding to different clusters) of a matrix of ...
Citrus is a computational technique developed for the analysis of high dimensional cytometry data sets. This package extracts, statistically analyzes, and visualizes marker expression from 'citrus' data. This code was used to generate data for Figures 3 and 4 in the forthcoming manuscript: Throm et al. “Identification of Enhanced Interferon-Gamma Signaling in Polyarticular Juvenile Idiopathic Arthritis with Mass Cytometry”, JCI-Insight. For more information on Citrus, please see: Bruggner et al. (2014) <doi:10.1073/pnas.1408792111>. To download the 'citrus' package, please see <https://github.com/nolanlab/citrus>.