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

## Documentation for package ‘sincell’ version 1.19.0

- 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()