PCA                     Parallelized PCA Analysis
Rphenograph             RphenoGraph clustering
add.confounder.variables
                        Add Confounder Variables
assess.cluster.similarity
                        Assess Cluster Similarity
cell.cycle.score        Compute Cell Cycle Score
cluster.analysis        Distributed Clustering Analysis
controlled.mean.score   Compute Controlled Activation Score
download_LCMV           Download Example Dataset
filter_cluster_data     Remove selected clusters
find_neighbors          K Nearest Neighbour Search
get.cluster.names       Get/Set Cluster Names by Marker Gene Expression
get.robust.cluster.similarity
                        Get Robust Cluster Similarity
get.robust.markers      Get Robust Marker
get.variable.genes      Identify Highly Variable Genes
initialize.project      Intialize the Project Environment
mitochondrial.score     Compute Mitochondrial Score
plot_PCA                Plot PCA results
plot_contour_overlay_tSNE
                        Plot Gene Expression on tSNE
plot_pair_scatter       Plot Pairwise Gene Scatter Plot
plot_simple_heatmap     Plot heatmap
read.data               Read and Preprocess Data
read.preclustered.datasets
                        Read Preclustered Datasets
read_10x_data           Read 10X Data
ribosomal.score         Compute Ribosomal Score
run_tSNE                Perform tSNE Analyses
setup_LCMV_example      Set up LCMV1 example
setup_pooled_env        Set up the pooled environment
summarize               Differential Expression and Figure Generation
visualize.cluster.cors.heatmaps
                        Visualize Correlation
visualize.cluster.similarity.stats
                        Plot Similarity Results
