CoGAPS-package | CoGAPS: Coordinated Gene Activity in Pattern Sets |
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 |
CoGAPS | CoGAPS Matrix Factorization Algorithm |
CoGapsFromCheckpoint | Restart CoGAPS from Checkpoint File |
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 |
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 |
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 |
reconstructGene | Reconstruct Gene |
reorderByPatternMatch | Reorder By Pattern Match |
reOrderBySet | reOrderBySet |
residuals | Plot of Residuals |
scCoGAPS | scCoGAPS |
scCoGapsFromCheckpoint | Restart a scCoGAPS run from a Checkpoint |
SimpSim.A | Simulated data |
SimpSim.D | Simulated data |
SimpSim.P | Simulated data |
SimpSim.result | Simulated Data Results |
SimpSim.S | Simulated data |
tf2ugFC | Gene sets defined by transcription factors defined from TRANSFAC. |