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

BuildSNN | Build Shared Nearest Neighbors matrix. From Seurat... |

CalcGeneModuleEffect | Calculate effect of perturbations on gene modules |

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

DesignMatrixGenotypes | Convert genotypes list to design matrix |

FilterData | Filter rows and columns of counts 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... |

GenotypeClusterChisq | Calculate chi-squared test of difference between each row of... |

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 |

ggcorrelation | Visualize correlation between two vectors |

ggheat | Plot matrix as heatmap. Options for clustering rows/columns |

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

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... |

PlotDims | Visualize t-SNE or PCA plots |

ReadData | Read data from either a tab separated values file or a 10X... |

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

UnflattenCellGenotypes | Convert genotypes from named vector to list |

UnflattenDataframe | Convert dataframe to matrix, specifying all column names |

WriteGenesets | Write genesets from list to gmt file |

WriteGenotypes | Write genotypes to csv file |

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