Package index • presto

Wilcoxon and auROC

Single-cell marker discovery with the rank-sum test.

wilcoxauc(): Fast Wilcoxon rank-sum test and auROC across groups
top_markers(): Top markers per group from wilcoxauc results

Pseudobulk differential expression

Collapse cells to per-donor pseudobulks and run DESeq2 across them.

collapse_counts(): Collapse a single-cell count matrix into pseudobulks
pseudobulk_deseq2(): Pseudobulk differential expression with DESeq2
top_markers_dds(): Top markers per group from pseudobulk DESeq2 results
summarize_dge_pairs(): Summarize directional pairwise DGE results
pseudobulk_one_vs_all(): Pseudobulk DESeq2: one-vs-all contrasts
pseudobulk_pairwise(): Pseudobulk DESeq2: pairwise contrasts
pseudobulk_within(): Pseudobulk DESeq2: within-group contrasts

Matrix utilities

Group-wise reductions used internally by wilcoxauc().

sumGroups(): Group-wise sum of a matrix along one axis
nnzeroGroups(): Group-wise non-zero counts of a matrix along one axis
rank_matrix(): Column-wise tied ranks of a matrix
compute_hash(): Compute a unique integer hash for each row of a data.frame

Demo data

Generators for tiny Seurat / SingleCellExperiment objects, built on the fly for the wilcoxauc() dispatch tests and examples.

toy_seurat(): Toy Seurat object for examples and tests
toy_sce(): Toy SingleCellExperiment object for examples and tests