Package: presto 1.0.0

Kamil Slowikowski

presto: Fast Functions for Differential Expression using Wilcox and AUC

Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment.

Authors:Ilya Korsunsky [aut], Aparna Nathan [aut], Nghia Millard [aut], Soumya Raychaudhuri [aut], Kamil Slowikowski [cre, ctb], Austin Hartman [ctb]

presto_1.0.0.tar.gz
presto_1.0.0.zip(r-4.7)presto_1.0.0.zip(r-4.6)presto_1.0.0.zip(r-4.5)
presto_1.0.0.tgz(r-4.6-x86_64)presto_1.0.0.tgz(r-4.6-arm64)presto_1.0.0.tgz(r-4.5-x86_64)presto_1.0.0.tgz(r-4.5-arm64)
presto_1.0.0.tar.gz(r-4.7-arm64)presto_1.0.0.tar.gz(r-4.7-x86_64)presto_1.0.0.tar.gz(r-4.6-arm64)presto_1.0.0.tar.gz(r-4.6-x86_64)
presto_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
presto/json (API)
NEWS

# Install 'presto' in R:
install.packages('presto', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunogenomics/presto/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • exprs - Small gene expression matrix
  • object_sce - SingleCellExperiment object with fake data
  • object_seurat - Seurat V3 object with fake data
  • y - Group labels for observations in gene expression matrix

On CRAN:

Conda:

cpp

7.70 score 212 stars 1.2k scripts 14 exports 25 dependencies

Last updated from:a24772a135. Checks:3 WARNING, 2 OK, 8 NOTE. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING246
linux-devel-x86_64WARNING279
source / vignettesOK304
linux-release-arm64NOTE265
linux-release-x86_64NOTE263
macos-release-arm64NOTE167
macos-release-x86_64NOTE412
macos-oldrel-arm64NOTE130
macos-oldrel-x86_64NOTE358
windows-develWARNING237
windows-releaseNOTE195
windows-oldrelNOTE232
wasm-releaseOK186

Exports:%>%collapse_countscompute_hashnnzeroGroupspseudobulk_deseq2pseudobulk_one_vs_allpseudobulk_pairwisepseudobulk_withinrank_matrixsumGroupssummarize_dge_pairstop_markerstop_markers_ddswilcoxauc

Dependencies:clicpp11data.tabledplyrgenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RcppRcppArmadillorlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Quick start to presto

Ilya Korsunsky

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2022-11-10
Started: 2019-05-07

Readme and manuals

Help Manual

Help pageTopics
Collapse counts based on multiple categorical metadata columnscollapse_counts
Compute unique hash for each row of data.framecompute_hash
Small gene expression matrixexprs
nnzeroGroupsnnzeroGroups nnzeroGroups.dgCMatrix nnzeroGroups.matrix
SingleCellExperiment object with fake dataobject_sce
Seurat V3 object with fake dataobject_seurat
Pseudobulk DESeq2pseudobulk_deseq2
Pseudobulk one versus allpseudobulk_one_vs_all
Pseudobulk pairwisepseudobulk_pairwise
Pseudobulk withinpseudobulk_within
rank_matrixrank_matrix rank_matrix.dgCMatrix rank_matrix.matrix
sumGroupssumGroups sumGroups.dgCMatrix sumGroups.matrix
Summarize differential gene expression pairssummarize_dge_pairs
Get top n markers from wilcoxauctop_markers
Get top n markers from pseudobulk DESeq2top_markers_dds
Fast Wilcoxon rank sum test and auROCwilcoxauc wilcoxauc.default wilcoxauc.Seurat wilcoxauc.seurat wilcoxauc.SingleCellExperiment
Group labels for observations in gene expression matrixy