Man pages for sctransform
Variance Stabilizing Transformations for Single Cell UMI Data

compare_expressionCompare gene expression between two groups
correctCorrect data by setting all latent factors to their median...
correct_countsCorrect data by setting all latent factors to their median...
diff_mean_testNon-parametric differential expression test for sparse...
diff_mean_test_conservedFind differentially expressed genes that are conserved across...
generateGenerate data from regularized models.
get_model_varReturn average variance under negative binomial model
get_nz_median2Get median of non zero UMIs from a count matrix
get_residualsReturn Pearson or deviance residuals of regularized models
get_residual_varReturn variance of residuals of regularized models
is_outlierIdentify outliers
make.sparseConvert a given matrix to dgCMatrix
pbmcPeripheral Blood Mononuclear Cells (PBMCs)
plot_modelPlot observed UMI counts and model
plot_model_parsPlot estimated and fitted model parameters
robust_scaleRobust scale using median and mad
robust_scale_binnedRobust scale using median and mad per bin
row_gmeanGeometric mean per row
row_varVariance per row
smooth_via_pcaSmooth data by PCA
umifyQuantile normalization of cell-level data to match typical...
umify_dataTransformation functions for umify
vstVariance stabilizing transformation for UMI count data
sctransform documentation built on Oct. 19, 2023, 9:08 a.m.