Package index • recall

Main Clustering Functions

Core functions for calibrated clustering

FindClustersRecall(): Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).

FindClustersCountsplit(): Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).

Seurat Integration

Helper functions for Seurat workflow

seurat_workflow(): Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).

get_seurat_obj_with_artificial_variables(): Returns a Seurat object that contains additional (fake) RNA expression counts.

Knockoff Filter

Statistical methods for FDR control

compute_knockoff_filter(): Returns the genes selected by the knockoff filter

Distribution Estimation

Parameter estimation for null distributions

estimate_zi_poisson(): Maximum likelihood estimation for the zero-inflated Poisson distribution with Poisson parameter lambda and zero proportion prop.zero.

estimate_negative_binomial(): Maximum likelihood estimation for the negative binomial distribution.

estimate_zi_poisson_copula() estimate_negative_binomial_copula() estimate_poisson_copula() estimate_gaussian_copula(): todo

rzipoisson(): Random data generation for the zero-infalted Poisson distribution with Poisson parameter lambda and zero proportion prop.zero.