# Statistical methods for analysing single cell RNA-seq data

## Documentation for package ‘speckle’ version 1.13.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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