A Tool for the Analysis of Tumour Therapeutic Heterogeneity in single-cell RNA-seq

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Documentation for package ‘beyondcell’ version 1.3.3

Help Pages

bc4Squares Drawns a 4 squares plot
bcAddMetadata Add new metadata to an existing beyondcell object
bcCellCycle Plots a violindot of the BCS grouped by cell cycle phase
bcClusters Plots a UMAP reduction coloured by metadata information
bcHistogram Plots a histogram with the BCS of the signature of interest
bcMerge Merges two beyondcell objects
bcRanks Ranks the signatures from most sensitive to least sensitive
bcRecompute Recomputes a beyondcell object
bcRegressOut Regresses out unwanted effects from BCS
bcScore Computes the BCS
bcSignatures Plots a UMAP reduction coloured by BCS or gene expression values
bcSubset Subsets a beyondcell object
bcUMAP Computes a UMAP projection and therapeutic clusters using the BCS
beyondcell Beyondcell class
beyondcell-class Beyondcell class
BreakString Breaks a string into several lines
CaseFraction Returns the fraction of each case type in the input
center_scale_colour_stepsn Creates a centred sequential binned colour gradient
colMinus Computes the column substraction
CreatebcObject Creates a new beyondcell object
FindDrugs Returns a dataframe with information about the input drugs
GenerateGenesets Creates a geneset object
geneset Geneset class
geneset-class Geneset class
GetIDs Returns the IDs that match the specified filter's values
GetStatistics Computes the BCS' statistics and ranks
get_colour_steps Returns a vector of 5 colours
ListFilters Returns all the possible values for the specified filter
Mean.Med.SD Computes the mean, the median and the sd of a vector
minus Substracts to the first element of a vector the rest of elements
rankSigs Returns the first/last n ranked signatures
SwitchPoint Computes the switch point