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 |