Statistical methods for analysing single cell RNA-seq data

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Documentation for package ‘speckle’ version 1.4.0

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

Help Pages

.extractSCE	Extract metadata from 'SingleCellExperiment' object
.extractSeurat	Extract metadata from 'Seurat' object
convertDataToList	Convert counts or proportions matrix to list object for propeller
estimateBetaParam	Estimate the parameters of a Beta distribution
estimateBetaParamsFromCounts	Estimate parameters of a Beta distribution from counts
getTransformedProps	Calculates and transforms cell type proportions
ggplotColors	Output a vector of colours based on the ggplot colour scheme
normCounts	Normalise a counts matrix to the median library size
pbmc_props	Cell type proportions from single cell PBMC data
plotCellTypeMeanVar	Plot cell type counts means versus variances
plotCellTypeProps	Plot cell type proportions for each sample
plotCellTypePropsMeanVar	Plot cell type proportions versus variances
propeller	Finding statistically significant differences in cell type proportions
propeller.anova	Performs F-tests for transformed cell type proportions
propeller.ttest	Performs t-tests of transformed cell type proportions
speckle_example_data	Generate example data