R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

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Documentation for package ‘sincell’ version 1.25.0

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ExpressionMatrix Single-cell expression data for genes differentially expressed in differentiating human skeletal muscle myoblasts cells
f_distance2vector Conversion of the lower triangular matrix of a distance matrix into an array
geneset.list Example of a geneset collection
knnalgorithm Auxiliary function for KNN and IMC algorithms
pseudoreplicatesbymodel Auxiliary function of sc_InSilicoCellsReplicatesObj function used when its parameter method="lognormal-3parameters"
pseudoreplicatesbynoise Auxiliary function of sc_InSilicoCellsReplicatesObj function used when its parameter method="variance.deciles"
pseudoreplicatesbynoise_cv2 Auxiliary function of sc_InSilicoCellsReplicatesObj function used when its parameter method="cv2.deciles"
sc_AssociationOfCellsHierarchyWithAGeneSet Association of a cell-state hierarchy with a functional gene set
sc_clusterObj Clustering of individual cells based on a metric of choice
sc_ComparissonOfGraphs Comparisson of graphs
sc_DimensionalityReductionObj Dimensionality reduction of an expression matrix
sc_distanceObj Assessment of a cell-to-cell distance matrix with a metric of choice
sc_GraphBuilderObj Graph building function for assessment of cell-state hierarchies
sc_InitializingSincellObject Function to initialize a sincell object
sc_InSilicoCellsReplicatesObj In silico generation of replicates of individual cells
sc_marker2color Palette of colors from the expression values of a marker gene
sc_StatisticalSupportByGeneSubsampling Statistical support of cell-state hierarchies by gene subsampling
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates Statistical support of cell-state hierarchies by random cell substitution with in silico-generated cell replicate
sstalgorithm Auxiliary function for SST algorithm within function sc_GraphBuilderObj()