Decomposition of Bulk Expression with Single-Cell Sequencing

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Documentation for package ‘BisqueRNA’ version 1.0.5

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

Help Pages

CalculateSCCellProportions	Calculate cell proportions based on single-cell data
CorTri	Correlate columns of data frame
CountsToCPM	Convert counts data in Expression Set to counts per million (CPM)
EstimatePCACellTypeProportions	Estimate cell type proportions using first PC of expression matrix
FilterUnexpressedGenes	Remove genes in Expression Set with zero expression in all samples
FilterZeroVarianceGenes	Remove genes in Expression Set with zero variance across samples
GenerateSCReference	Generate reference profile for cell types identified in single-cell data
GetCTP	Return cell type proportions from bulk
GetNumGenes	Get number of genes to use with no weighted information
GetNumGenesWeighted	Get number of genes to use with weighted PCA
GetOverlappingGenes	Find overlapping genes in single-cell data, bulk data, and marker genes
GetOverlappingSamples	Find overlapping samples in single-cell and bulk data
GetUniqueMarkers	Get unique markers present in only 1 cell type
MarkerBasedDecomposition	Performs marker-based decomposition of bulk expression using marker genes
ReferenceBasedDecomposition	Performs reference-based decomposition of bulk expression using single-cell data
SemisupervisedTransformBulk	Transforms bulk expression of a gene using only single-cell data
SeuratToExpressionSet	Converts Seurat object to Expression Set
SimulateBarcode	Simulate barcode for decomposition illustration
SimulateData	Simulate data for decomposition illustration
SupervisedTransformBulk	Transforms bulk expression of a gene given overlapping data