Single Cell Overview of Normalized Expression data

biplot_color | Function for biplotting with no point labels and with points... |

biplot_interactive | Interactive biplot |

CLR_FN | Centered log-ratio (CLR) normalization wrapper function |

control_genes | Data: Positive and Negative Control Genes |

DESEQ_FN | Relative log-expression (RLE; DESeq) scaling normalization... |

estimate_ziber | Parameter estimation of zero-inflated bernoulli model |

factor_sample_filter | Factor-based Sample Filtering: Function to filter single-cell... |

FQ_FN | Full-quantile normalization wrapper function |

get_bio | Get Factor of Biological Conditions and Batch |

get_design | Retrieve Design Matrix |

get_negconruv | Get Negative and Positive Controls |

get_normalized | Retrieve Normalized Matrix |

get_params | Extract scone parameters |

get_qc | Get Quality Control Matrix |

get_scores | Extract scone scores |

impute_expectation | Imputation of zero abundance based on general zero-inflated... |

impute_null | Null or no-op imputation |

lm_adjust | Linear Adjustment Normalization |

make_design | Make a Design Matrix |

metric_sample_filter | Metric-based Sample Filtering: Function to filter single-cell... |

scone | Normalize Expression Data and Evaluate Normalization... |

scone_easybake | Wrapper for Running Essential SCONE Modules |

SconeExperiment-class | Class SconeExperiment |

sconeReport | SCONE Report Browser: Browse Evaluation of Normalization... |

score_matrix | SCONE Evaluation: Evaluate an Expression Matrix |

SCRAN_FN | Simple deconvolution normalization wrapper |

select_methods | Get a subset of normalizations from a SconeExperiment object |

simple_FNR_params | Fit Simple False-Negative Model |

SUM_FN | Sum scaling normalization function |

TMM_FN | Weighted trimmed mean of M-values (TMM) scaling normalization... |

UQ_FN | Upper-quartile (UQ) scaling normalization wrapper function |

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