Man pages for CoGAPS/CoGAPS
Coordinated Gene Activity in Pattern Sets

binaryABinary Heatmap for Standardized A Matrix
calcCoGAPSStatCalculate Gene Set Statistics
calcGeneGSStatProbability Gene Belongs in Gene Set
calcZCompute Z-Score Matrix
cellMatchRcellMatchR
CoGAPSCoGAPS Matrix Factorization Algorithm
CoGapsFromCheckpointRestart CoGAPS from Checkpoint File
CoGAPS-packageCoGAPS: Coordinated Gene Activity in Pattern Sets
computeGeneGSProbCompute Gene Probability
createGWCoGAPSSetsCreate Gene Sets for GWCoGAPS
createscCoGAPSSetsCreate Gene Sets for scCoGAPS
displayBuildReportDisplay Information About Package Compilation
gapsMapRunBackwards Compatibility with v2
gapsRunBackwards Compatibility with v2
generateSeedsGenerate Seeds for Multiple Concurrent Runs
GIST.DSample GIST gene expression data from Ochs et al. (2009).
GIST.SSample GIST gene expression data from Ochs et al. (2009).
GSetsSimulated dataset to quantify gene set membership.
GWCoGAPSGWCoGAPS
GWCoGapsFromCheckpointRestart a GWCoGaps Run from Checkpoint
patternMarkerspatternMarkers
patternMatch4ParallelpatternMatch4Parallel
patternMatcherPatternMatcher Shiny Ap
plotAtomsPlot Number of Atoms
plotDiagDiagnostic Plots
plotGAPSPlot Decomposed A and P Matrices
plotPPlot the P Matrix
plotPatternMarkersplotPatternMarkers
plotSmoothPatternsPlot Smooth Patterns
postFixed4ParallelPost Processing of Parallel Output
postFixed4SCPost Processing of Parallel Output
reconstructGeneReconstruct Gene
reorderByPatternMatchReorder By Pattern Match
reOrderBySetreOrderBySet
residualsPlot of Residuals
scCoGAPSscCoGAPS
scCoGapsFromCheckpointRestart a scCoGAPS run from a Checkpoint
SimpSim.ASimulated data
SimpSim.DSimulated data
SimpSim.PSimulated data
SimpSim.resultSimulated Data Results
SimpSim.SSimulated data
tf2ugFCGene sets defined by transcription factors defined from...
CoGAPS/CoGAPS documentation built on July 28, 2018, 3:14 a.m.