Man pages for jenzopr/singlecellutils
Utility functions for single-cell data
| add_clustering | Add a clustering |
| add_transition_index | Adds the cirtical transition index to the object. |
| bootstrap_transition_index | Run non-parametric bootstrapping for critical transition... |
| boot_subsample | Helper function for non-parametric subsampling |
| calculate_qc_map | Calculates a 2D QC map of cells based on quality features |
| colon-equals | rlang quasiquotation |
| compute_transition_index | Calculate the critical transition index for cells in a... |
| construct_filters | Conveneince function to construct a list of filter... |
| constructHexNeighborhood | Construct the neighborhood of a hexagonal r*q matrix |
| discover_element | Convenience function to discover elements in 'what' in a... |
| dot-lrde_pval | Function to perform logistic regression test |
| filter | Functions to filter features or samples using 'genefilter'. |
| filterfunctions | Basic filter functions |
| grapes-greater-than-grapes | magrittr forward-pipe operator |
| hdbscan | Conveinience function to perform HDBSCAN via reticulate. |
| hdbscan_ | Conveinience function to perform HDBSCAN via reticulate. |
| isomds | Conveinience function to run isoMDS on a SingleCellExperiment... |
| lrde_test | Tests differential expression/accessibility using logistic... |
| map.init | Initializes a SOM map with the first two PCA components in a... |
| map.init.local | Initializes a SOM map with the first two PCA components in a... |
| neuron_1k_v3 | 1k Brain Cells from an E18 Mouse (v3 chemistry) |
| n_filterfun | A custom 'filterfun' that creates a n-FALSE exiting function... |
| plotComplexHeatmap | Creating a ComplexHeatmap from expression or reducedDim data... |
| plotSilhouette | Plots a silhouette plot |
| reduce_dimension | Performs dimension reduction and adds results to the given... |
| scaterIsOutlier | A filter function with bindings for parameters for... |
| scSOM | Calculates a (weighted) self-organizing map |
| svd | Approximate or randomized singular value decomposition |
| tf_idf | Calculates the term frequency-inverse document frequency. |
| umap | Conveinience function to perform UMAP via reticulate. |
