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 1.30.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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()