Man pages for BaderLab/scClustViz
Differential Expression-based scRNAseq Cluster Assessment and Viewing

addCellMarkersToCGSAdd gene symbols and cell type marker information to cluster...
CalcAllSCVPrepare all cluster solutions for visualization with...
CalcCGSCalculate cluster-wise gene statistics for sCVdata
CalcDEcombnPerforms DE testing between pairs of clusters in sCVdata
CalcDEvsRestCalculates one vs. all DE tests for sCVdata
CalcSCVCreate sCVdata object with calculation results for a cluster
CalcSilhouetteCalculates silhouette widths for all cells in sCVdata
cosineSimComputes the cosine similarity between two vectors
DEdistCalculate inter-cluster distances
DEdistNNDetermine nearest neighbouring clusters
DEmarkerFind marker genes for each cluster
DEneighbFind differentially expressed genes between nearest...
dotplotDEgenesscClustViz plot helper function: Return DE genes per cluster
findKeyTypeAutomatically determines keytype for AnnotationDb lookup
fx_calcCGSInternal fx for cluster-wise gene statistics
fx_calcCGS_BPInternal fx for cluster-wise gene statistics using...
fx_calcDEcombnInternal fx to calculate DE between combinations of clusters
fx_calcDEcombn_BPInternal fx to calculate DE between combinations of clusters...
fx_calcDEvsRestInternal fx to perform one vs all DE testing
fx_calcDEvsRest_BPInternal fx to perform one vs all DE testing using...
fx_calcDist_cellEmbInternal function for distance between clusters from cell...
fx_calcDist_geneExprInternal function for distance between clusters by gene...
fx_calcDist_numDEInternal function for distance between clusters by number of...
fx_calcDist_scoreDEInternal function for distance between clusters by DE score.
fx_calcEScombnInternal fx to calculate genes used for deVS calculation
fx_calcESvsRestInternal fx to calculate logGER for DEvsRest calculation
fx_calcESvsRest_BPInternal fx to calculate logGER for DEvsRest calculation...
fx_calcMarkerInternal function to find marker genes for each cluster
fx_calcNeighbInternal function to find DE genes between nearest...
fx_calcSilhouetteInternal fx to call 'silhouette' for sCVdata.
getEmbGet cell embeddings from input data object
getExprGet gene expression matrix from input data object
getMDGet metadata from input data object
hasEmbList cell embedding types from input data object
labelCellTypesscClustViz helper fx: Add predicted cell type names to...
map2symbolMaps gene identifiers to official gene symbol
meanLogXComputes the mean of log-scaled values
origin.label.distInternal fx to calc dist from point to label end
overlap.edgeInternal fx to calc overlap of label and plot edge
overlap.proportion.pointInternal fx to calc relative overlap of labels
plot_clusterGenes_DEgenesscClustViz plot: Plot within-cluster gene expression...
plot_clusterGenes_markersscClustViz plot: Plot within-cluster gene expression...
plot_clusterGenes_searchscClustViz plot: Plot within-cluster gene expression...
plot_clustSepscClustViz plot: Cluster separation boxplots
plot_compareClustsscClustViz plot: Volcano and MA-style plots to compare...
plot_deDotplotscClustViz plot: Plot gene expression dotplots.
plot_GEboxplotscClustViz plot: Compare gene expression across clusters
plot_mdComparescClustViz plot: Plot to compare cell metadata
plot_mdPerClustscClustViz plot: Plot to view cellular metadata by cluster
plot_silscClustViz plot: Silhouette plot
plot_tsnescClustViz plot: Plot cell embedding in 2D
runShinyRun the scClustViz Shiny app
scClustVizscClustViz: A package for interactive exploration of scRNAseq...
sCVdata-classAnalysis results for the scClustViz app
sCVparams-classParameters used in the sCVdata class and methods.
spreadLabels2Prevent overlapping labels
tsne_labelsscClustViz plot element: Cluster names on cluster centroid.
BaderLab/scClustViz documentation built on July 15, 2019, 10:08 a.m.