Analyzes effect of genetic perturbations on the transcriptome using a linear model. Based on the MIMOSCA python package (https://github.com/asncd/MIMOSCA)

CalcClusterEnrich | Calculate cluster enrichment with logistic regression |

CalcClusterEnrichPvals | Calculate cluster enrichment with logistic regression |

CalcGeneModuleEffect | Calculate effect of perturbations on gene modules |

CalcGlmnet | Calculate penalized linear regression with glmnet |

CalcGlmnetPvals | Calculate regression coefficients and p-values via... |

CleanDesignCtrl | Filters out cells that belong to control genotype and other... |

DesignMatrixGenotypes | Convert genotypes list to design matrix |

FilterGenesets | Filter genesets by minimum, maximum number of genes |

FisherEnrich | Use Fisher's exact test to calculate enrichment for count... |

FlattenGenotypeList | Convert genotypes dictionary from list to named vector. All... |

GenesetDotPlot | Dot plot visualization |

GenotypeClusterCounts | Counts the number of cells in each genotype x cluster... |

GenotypeClusterPvals | Use Fisher's exact test to calculate enrichment for each... |

GetCoefMatrix | Extract coefficient matrix from a multigaussian glmnet object |

ggBarplot | Make simple barplot from vector |

hello | Hello, World! |

LoadGenesets | Read genesets from gmt file to list format |

MultipleFisherEnrich | Count over-enrichment for a list of gene markers |

MultipleGSEAEnrich | GSEA over-enrichment test using liger |

PadDesignMatrix | Pad design matrix with zeros for cells without a called... |

PlotCorrelation | Visualize correlation between two vectors |

PlotHexBin | Visualize correlation between two vectors with density plot.... |

PlotViolin | Violin plot (adapted from Seurat) |

ReadGenotypes | Read in genotypes dictionary from csv file. Returns an R... |

UnflattenCellGenotypes | Convert genotypes from named vector to list |

WriteGenesets | Write genesets from list to gmt file |

WriteGenotypes | Write genotypes to csv file |

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