Man pages for sctransform
Variance Stabilizing Transformations for Single Cell UMI Data
| clip_matrix_values | Clip matrix values to specified range |
| close_progress_bar | Close progress bar |
| compare_expression | Compare gene expression between two groups |
| correct | Correct data by setting all latent factors to their median... |
| correct_counts | Correct data by setting all latent factors to their median... |
| diff_mean_test | Non-parametric differential expression test for sparse... |
| diff_mean_test_conserved | Find differentially expressed genes that are conserved across... |
| generate | Generate data from regularized models. |
| get_model_formula | Extract model formula from model string |
| get_model_var | Return average variance under negative binomial model |
| get_nz_median2 | Get median of non zero UMIs from a count matrix |
| get_residuals | Return Pearson or deviance residuals of regularized models |
| get_residual_var | Return variance of residuals of regularized models |
| is_outlier | Identify outliers |
| make.sparse | Convert a given matrix to dgCMatrix |
| pbmc | Peripheral Blood Mononuclear Cells (PBMCs) |
| plot_model | Plot observed UMI counts and model |
| plot_model_pars | Plot estimated and fitted model parameters |
| prepare_regressor_data | Prepare regressor data from vst object and cell attributes |
| 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 |
| setup_progress_bar | Setup progress bar for batch processing |
| smooth_via_pca | Smooth data by PCA |
| umify | Quantile normalization of cell-level data to match typical... |
| umify_data | Transformation functions for umify |
| update_progress_bar | Update progress bar |
| vst | Variance stabilizing transformation for UMI count data |
