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BisqueRNA

Decomposition of Bulk Expression with Single-Cell Sequencing

Provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples. For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.

Functions (20)

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

BisqueRNA

Decomposition of Bulk Expression with Single-Cell Sequencing

v1.0.4
GPL-3
Authors
Brandon Jew [aut, cre], Marcus Alvarez [aut]
Initial release

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