Variance Stabilizing Transformations for Single Cell UMI Data

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_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 |

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 |

umify | Quantile normalization of cell-level data to match typical... |

umify_data | Transformation functions for umify |

vst | Variance stabilizing transformation for UMI count data |

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