A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

add_import | add_import |

annotate_clusters | annotate_clusters functionally annotates the identified... |

bootstrap_parallel | BootStrap runs for both scGPS training and prediction with... |

bootstrap_prediction | BootStrap runs for both scGPS training and prediction |

calcDist | Compute Euclidean distance matrix by rows |

calcDistArma | Compute Euclidean distance matrix by rows |

clustering | HC clustering for a number of resolutions |

clustering_bagging | HC clustering for a number of resolutions |

CORE_bagging | Main clustering SCORE (CORE V2.0) Stable Clustering at... |

CORE_clustering | Main clustering CORE V2.0 updated |

CORE_subcluster | sub_clustering (optional) after running CORE 'test' |

day_2_cardio_cell_sample | One of the two example single-cell count matrices to be used... |

day_5_cardio_cell_sample | One of the two example single-cell count matrices to be used... |

distvec | Compute Distance between two vectors |

find_markers | find marker genes |

find_optimal_stability | Find the optimal cluster |

find_stability | Calculate stability index |

mean_cpp | Calculate mean |

new_scGPS_object | new_scGPS_object |

new_summarized_scGPS_object | new_summarized_scGPS_object |

PCA | PCA |

plot_CORE | Plot dendrogram tree for CORE result |

plot_optimal_CORE | plot one single tree with the optimal clustering result |

plot_reduced | plot reduced data |

predicting | Main prediction function applying the optimal ElasticNet and... |

PrinComp_cpp | Principal component analysis |

rand_index | Calculate rand index |

rcpp_Eucl_distance_NotPar | Function to calculate Eucledean distance matrix without... |

rcpp_parallel_distance | distance matrix using C++ |

reformat_LASSO | summarise bootstrap runs for Lasso model, from 'n' bootstraps |

sub_clustering | sub_clustering for selected cells |

subset_cpp | Subset a matrix |

summary_accuracy | get percent accuracy for Lasso model, from 'n' bootstraps |

summary_deviance | get percent deviance explained for Lasso model, from 'n'... |

summary_prediction_lasso | get percent deviance explained for Lasso model, from 'n'... |

summary_prediction_lda | get percent deviance explained for LDA model, from 'n'... |

top_var | select top variable genes |

tp_cpp | Transpose a matrix |

training | Main model training function for finding the best model that... |

training_gene_sample | Input gene list for training 'scGPS', e.g. differentially... |

tSNE | tSNE |

var_cpp | Calculate variance |

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