Package index
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compute_log_fold_change() - Compute the log2 fold change and its standard error
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compute_posterior() - Compute posterior according to Gamma-Poisson model
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compute_posterior(<default>) - Compute posterior according to Gamma-Poisson model for matrices and sparse matrices.
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compute_posterior(<eSVD>) - Compute posterior according to Gamma-Poisson model for eSVD object
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compute_pvalue() - Compute p-values
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compute_test_per_gene() - Gene-wise posterior + test statistic + p-value without storing posterior matrices
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compute_test_statistic() - Compute test statistics
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compute_test_statistic(<default>) - Compute test statistics for matrices
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compute_test_statistic(<eSVD>) - Compute test statistics for eSVD object
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eSVD() - Run the full eSVD-DE pipeline on a Seurat object
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eSVD_helper() - Run eSVD-DE on a Seurat object, with cohort filtering and gene status
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estimate_nuisance() - Estimate nuisance values
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estimate_nuisance(<default>) - Estimate nuisance values for matrix or sparse matrices.
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estimate_nuisance(<eSVD>) - Estimate nuisance values for eSVD objects (i.e., over-dispersion)
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filter_cohort() - Filter a cohort before running eSVD-DE
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fisher_test() - Fisher's exact test
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format_covariates() - Format covariates
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gandal_df - Gandal et al. results
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generate_data() - Generate data
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generate_null() - Generate null data
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housekeeping_df - Hounkpe et al. housekeeping genes
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initialize_esvd() - Initialize eSVD
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multtest() - Perform multiple-testing adjustment using Efron's empirical null
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opt_esvd() - Optimize eSVD
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opt_esvd(<default>) - Optimize eSVD for matrices or sparse matrices.
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opt_esvd(<eSVD>) - Optimize eSVD for eSVD objects
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plot_fitted_vs_observed() - Plot the fitted count against the observed count
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plot_nuisance() - Plot each gene's nuisance rate against a summary of the gene
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recompute_pvalue() - Redo the test at another cap on the nuisance rate, without fitting again
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reparameterization_esvd_covariates() - Reparameterize eSVD object
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report_results() - Report the DE results from eSVD
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sfari_df - SFARI genes
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velmeshev_gene_df - Velmeshev et al. DEGs