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]

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presto.pdf |presto.html
presto/json (API)
NEWS

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

Peer review:

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:

14 exports 140 stars 4.70 score 26 dependencies

Last updated 3 months agofrom:7636b3d0465c468c35853f82f1717d3a64b3c8f6

Exports:%>%collapse_countscompute_hashnnzeroGroupspseudobulk_deseq2pseudobulk_one_vs_allpseudobulk_pairwisepseudobulk_withinrank_matrixsumGroupssummarize_dge_pairstop_markerstop_markers_ddswilcoxauc

Dependencies:clicpp11data.tabledplyrfansigenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RcppRcppArmadillorlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Quick start to presto

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Jun 16 2024.

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
prestopresto
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