SCEVAN                  SCEVAN: R package that automatically classifies
                        the cells in the scRNA data by segregating
                        non-malignant cells of tumor microenviroment
                        from the malignant cells. It also infers the
                        copy number profile of malignant cells,
                        identifies subclonal structures and analyses
                        the specific and shared alterations of each
                        subpopulation.
annotateGenes           annotateGenes Annotate genes with genomic
                        coordinates with reference to hg38 using
                        Ensembl based annotation package
annoteBandOncoHeat      annoteBandOncoHeat Annotate with chromosome
                        bands the data frame with difference copy
                        number alterations between subclones
classifyCluster         classifyCluster Classify the two major clusters
                        of CNA matrix on the basis of confident normal
                        cells
classifyTumorCells      classifyTumorCells Classify tumour and normal
                        cells from the raw count matrix, using normal
                        cells in the matrix or by subtracting a
                        synthetic baseline from the matrix if there are
                        no normal cells in the matrix.
computeCNAmtx           computeCNAmtx computed the CNA matrix using the
                        break points obtained from segmentation
getBreaksVegaMC         getBreaksVegaMC Get SCEVAN segmentation of the
                        matrix.
getConfidentNormalCells
                        getConfidentNormalCells Get at most top 30
                        confident normal cells from count matrix.
multiSampleComparisonClonalCN
                        multiSampleComparisonClonalCN Compare the
                        clonal Copy Number of multiple samples.
pipelineCNA             pipelineCNA Executes the entire SCEVAN pipeline
                        that classifies tumour and normal cells from
                        the raw count matrix, infer the clonal profile
                        of cancer cells and looks for possible
                        sub-clones in the tumour cell matrix
                        automatically analysing the specific and shared
                        alterations of each subclone and a differential
                        analysis of pathways and genes expressed in
                        each subclone.
plotAllClonalCN         Title plotAllClonalCN
plotAllSubclonalCN      plotAllSubclonalCN Plot the copy number of each
                        subclone of a sample.
plotCNA_withAnnotCells
                        plotCNA_withAnnotCells allows generating a
                        heatmap of the copy number profile of each
                        cell, adding cell annotations as tracks on the
                        heatmap.
removeSyntheticBaseline
                        removeSyntheticBaseline Removes a synthetic
                        baseline from a tumour pure matrix
sortData                This function sorts a dataset file by the
                        genomic position of the probes.
top30classification     Get at most top 30 confident normal cells
