# Variance Stabilizing Transformations for Single Cell UMI Data

## Documentation for package ‘sctransform’ version 0.2.1

- DESCRIPTION file.

## Help Pages

compare_expression | Compare gene expression between two groups
correct | Correct data by setting all latent factors to their median values and reversing the regression model
correct_counts | Correct data by setting all latent factors to their median values and reversing the regression model
generate | Generate data from regularized models.
get_model_var | Return average variance under negative binomial model
get_residuals | Return Pearson or deviance residuals of regularized models
get_residual_var | Return variance of residuals of regularized models
is_outlier | Identify outliers
pbmc | Peripheral Blood Mononuclear Cells (PBMCs)
plot_model | Plot observed UMI counts and model
plot_model_pars | Plot estimated and fitted model parameters
robust_scale | Robust scale using median and mad
robust_scale_binned | Robust scale using median and mad per bin
row_gmean | Geometric mean per row
row_var | Variance per row
smooth_via_pca | Smooth data by PCA
vst | Variance stabilizing transformation for UMI count data