ArrangeData             Data trimming
CenterData              Data centering
CheckArguments_Impute   Argument check to Impute()
ChooseMethod            Method choice per gene
Combine                 Combine imputation methods
ComputeMSEGenewise      Computation of MSE per gene
CreateArgCheck          Argument check
CreateTrainData         Preparation of training data for method
                        evaluation
DataCheck_Matrix        Data check (matrix)
DataCheck_Network       Data check (network)
DataCheck_SingleCellExperiment
                        Data check (SingleCellExperiment)
DataCheck_TrLength      Data check (transcript length)
EvaluateMethods         Imputation method evaluation on training set
GetDropoutProbabilities
                        Get dropout probabilities
HandleBiologicalZeros   Get dropout probabilities
Impute                  Dropout imputation using different methods
ImputeBaseline          Impute using average expression across all
                        cells
ImputeDrImpute          Use DrImpute
ImputeNPDropouts        Helper function to
                        PseudoInverseSolution_percell
ImputeNetParallel       Network-based parallel imputation
ImputeNetwork           Network-based imputation
ImputePredictiveDropouts
                        Helper function to
                        PseudoInverseSolution_percell
ImputeSAVER             Use SAVER
MaskData                Masking of entries for performance evaluation
MaskerPerGene           Helper mask function
NormalizeRPM            RPM normalization
NormalizeTPM            TPM normalization
PseudoInverseSolution_percell
                        Network-based parallel imputation -
                        Moore-Penrose pseudoinversion
ReadData                Data read
ReturnChoice            Wrapper for return of EvaluateMethods()
ReturnOut               Wrapper for return of Impute()
SetBiologicalZeros      Set biological zeros
SplitData               Selection of samples for training
WriteCSV                Write csv file
WriteTXT                Write txt file
demo_data               Small dataset for example purposes
demo_net                Small regulatory network for example purposes
demo_sce                Small dataset for example purposes
network.coefficients    Transcriptome wide gene regulatory network
transcript_length       Table for transcript length calculations
