Decomposition of Bulk Expression with Single-Cell Sequencing


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Documentation for package ‘BisqueRNA’ version 1.0.5

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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