Fast Functions for Differential Expression Using Wilcoxon and AUC

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Documentation for package ‘presto’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

collapse_counts	Collapse a single-cell count matrix into pseudobulks
compute_hash	Compute a unique integer hash for each row of a data.frame
nnzeroGroups	Group-wise non-zero counts of a matrix along one axis
nnzeroGroups.dgCMatrix	Group-wise non-zero counts of a matrix along one axis
nnzeroGroups.matrix	Group-wise non-zero counts of a matrix along one axis
pseudobulk_deseq2	Pseudobulk differential expression with DESeq2
pseudobulk_one_vs_all	Pseudobulk DESeq2: one-vs-all contrasts
pseudobulk_pairwise	Pseudobulk DESeq2: pairwise contrasts
pseudobulk_within	Pseudobulk DESeq2: within-group contrasts
rank_matrix	Column-wise tied ranks of a matrix
rank_matrix.dgCMatrix	Column-wise tied ranks of a matrix
rank_matrix.matrix	Column-wise tied ranks of a matrix
sumGroups	Group-wise sum of a matrix along one axis
sumGroups.dgCMatrix	Group-wise sum of a matrix along one axis
sumGroups.matrix	Group-wise sum of a matrix along one axis
summarize_dge_pairs	Summarize directional pairwise DGE results
top_markers	Top markers per group from wilcoxauc results
top_markers_dds	Top markers per group from pseudobulk DESeq2 results
toy_sce	Toy SingleCellExperiment object for examples and tests
toy_seurat	Toy Seurat object for examples and tests
wilcoxauc	Fast Wilcoxon rank-sum test and auROC across groups
wilcoxauc.default	Fast Wilcoxon rank-sum test and auROC across groups
wilcoxauc.Seurat	Fast Wilcoxon rank-sum test and auROC across groups
wilcoxauc.seurat	Fast Wilcoxon rank-sum test and auROC across groups
wilcoxauc.SingleCellExperiment	Fast Wilcoxon rank-sum test and auROC across groups