CoGAPS                  CoGAPS Matrix Factorization Algorithm
CoGAPS-package          CoGAPS: Coordinated Gene Activity in Pattern
                        Sets
CoGapsFromCheckpoint    Restart CoGAPS from Checkpoint File
GIST.D                  Sample GIST gene expression data from Ochs et
                        al. (2009).
GIST.S                  Sample GIST gene expression data from Ochs et
                        al. (2009).
GSets                   Simulated dataset to quantify gene set
                        membership.
GWCoGAPS                GWCoGAPS
GWCoGapsFromCheckpoint
                        Restart a GWCoGaps Run from Checkpoint
SimpSim.A               Simulated data
SimpSim.D               Simulated data
SimpSim.P               Simulated data
SimpSim.S               Simulated data
SimpSim.result          Simulated Data Results
binaryA                 Binary Heatmap for Standardized A Matrix
calcCoGAPSStat          Calculate Gene Set Statistics
calcGeneGSStat          Probability Gene Belongs in Gene Set
calcZ                   Compute Z-Score Matrix
cellMatchR              cellMatchR
computeGeneGSProb       Compute Gene Probability
createGWCoGAPSSets      Create Gene Sets for GWCoGAPS
createscCoGAPSSets      Create Gene Sets for scCoGAPS
displayBuildReport      Display Information About Package Compilation
gapsMapRun              Backwards Compatibility with v2
gapsRun                 Backwards Compatibility with v2
generateSeeds           Generate Seeds for Multiple Concurrent Runs
patternMarkers          patternMarkers
patternMatch4Parallel   patternMatch4Parallel
patternMatcher          PatternMatcher Shiny Ap
plotAtoms               Plot Number of Atoms
plotDiag                Diagnostic Plots
plotGAPS                Plot Decomposed A and P Matrices
plotP                   Plot the P Matrix
plotPatternMarkers      plotPatternMarkers
plotSmoothPatterns      Plot Smooth Patterns
postFixed4Parallel      Post Processing of Parallel Output
postFixed4SC            Post Processing of Parallel Output
reOrderBySet            reOrderBySet
reconstructGene         Reconstruct Gene
reorderByPatternMatch   Reorder By Pattern Match
residuals               Plot of Residuals
scCoGAPS                scCoGAPS
scCoGapsFromCheckpoint
                        Restart a scCoGAPS run from a Checkpoint
tf2ugFC                 Gene sets defined by transcription factors
                        defined from TRANSFAC.
