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annotateCNVtree()
Annotate a Phylogenetic Tree with CNV Events
annotations_8um_to_16um()
Project 8µm Spatial Annotation onto 16µm Spots
CNVanalysis()
CNVanalysis Runs Copy Number Variation (CNV) analysis on a Seurat object or a list of Seurat objects.
CNVcalling()
CNVcalling Performs Copy Number Variation (CNV) analysis on a Seurat object.
CNVcallingList()
CNVcalling for a List of Seurat Objects Performs Copy Number Variation (CNV) analysis on a list of Seurat objects.
CNVclassification()
CNV Classification Classifies the CNV results into loss, gain, or no alteration for each observation and chromosome arm.
CNVcluster()
Perform CNV Clustering with Seurat Object
CNVPerChromosomeArm()
CNV Per Chromosome Arm Computes the CNV fraction of each spot/cell per chromosome arm, then stores the results into the metadata.
CNVtree()
Construct a Phylogenetic Tree from a Copy Number Variation (CNV) Matrix
compute_average_expression()
Compute average expression for patients
fastCNV()
fastCNV calls all of the internal functions needed to compute the putative CNV on a Seurat object or a list of Seurat objects
fastCNV_10XHD()
fastCNV_10XHD calls all of the internal functions needed to compute the putative CNV on a Seurat Visium HD object or a list of Seurat Visium HD objects
geneMetadata
Genes Data from Ensembl Version 113
generateCNVClonesMatrix()
Generate CNV Matrix for CNV Clusters by Chromosome Arm
getGenes()
Download Gene Information from Ensembl
plotCNVResults()
Plot CNV Results into a Heatmap Builds a heatmap to visualize the CNV results based on genomic scores.
plotCNVResultsHD()
Plot Visium HD CNV Results into a Heatmap Builds a heatmap to visualize the Visium HD CNV results based on genomic scores.
plotCNVtree()
Plot an Annotated Phylogenetic Tree with CNV Events
prepareCountsForCNVAnalysis()
Aggregate Observations by Cell Type for CNV Analysis Aggregates observations with the same cell types to increase counts per observation, improving Copy Number Variation (CNV) computation.