AugmentSigMatrix        Make an augmented signature matrix
LM22                    Leukocyte 22 data matrix
Licenses                Licenses required by Celgene legal
MGSM27                  Myeloma Genome Signature Matrix 27
SVMDECON                Support vector machine deconvolution
buildSeed               Build a deconvolution seed matrix, add the
                        proportional option
buildSpilloverMat       Build a spillover matrix
calcAcc                 Calculate prediction accuracy
clustWspillOver         Cluster with spillover
collapseCellTypes       Collapse cell types
estCellCounts.nPass     Deconvolve with an n-pass spillover matrix
estCellPercent          Wrapper for deconvolution methods
estCellPercent.DCQ      DCQ Deconvolution
estCellPercent.DeconRNASeq
                        DeconRNASeq deconvolution
estCellPercent.nnls     Non-negative least squares deconvolution
estCellPercent.proportionsInAdmixture
                        WGCNA::proportionsInAdmixture deconvolution
estCellPercent.spillOver
                        Estimate cell percentage from spillover
estCellPercent.svmdecon
                        SVMDECON deconvolution
findConvergenceIter     Find out at which iteration the results
                        converge, i.e. the mean results are stable.
gListFromRF             Build a gList using random forest
getF1mcc                Get f1 / mcc
getLM22cells            LM22 look up table
hierarchicalClassify    Hierarchical Deconvolution
hierarchicalSplit       Build hierarchical cell clusters.
loadMGSM27              Load MGSM27
loadModMap              LM22 to xCell LUT
loopTillConvergence     Loop testAllSigMatrices until convergence
matrixToGenelist        Make a GSVA genelist
meanResults             A meta analysis for the results from multiple
                        iterations
missForest.par          Use parallel missForest to impute missing
                        values.
plotKappas              Plot condition numbers
rankByT                 Rank genes for each cell type
remakeLM22p             Make an Augmented Signature Matrix
scSample                Build groupSize pools according to cellIDs
shrinkByKappa           Calculate conditions numbers for signature
                        subsets
shrinkSigMatrix         Shrink a signature matrix
spillToConvergence      Spillover to convergence
splitSCdata             Split a single cell dataset into multiple sets
testAllSigMatrices      Generate all the signature matrices one time
                        with the option to leave out half of the data
                        as a test set
weightNorm              SVMDECONV helper function
