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'))

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 146 stars 4.77 score 26 dependencies

Last updated 4 months agofrom:7636b3d046

Exports:%>%collapse_counts compute_hash nnzeroGroups pseudobulk_deseq2 pseudobulk_one_vs_all pseudobulk_pairwise pseudobulk_within rank_matrix sumGroups summarize_dge_pairs top_markers top_markers_dds wilcoxauc

Dependencies:cli cpp11 data.table dplyr fansi generics glue lattice lifecycle magrittr Matrix pillar pkgconfig purrr R6 Rcpp RcppArmadillo rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Quick start to presto

Ilya Korsunsky

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

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Collapse counts based on multiple categorical metadata columns	collapse_counts
Compute unique hash for each row of data.frame	compute_hash
Small gene expression matrix	exprs
nnzeroGroups	nnzeroGroups nnzeroGroups.dgCMatrix nnzeroGroups.matrix
SingleCellExperiment object with fake data	object_sce
Seurat V3 object with fake data	object_seurat
presto	presto
Pseudobulk DESeq2	pseudobulk_deseq2
Pseudobulk one versus all	pseudobulk_one_vs_all
Pseudobulk pairwise	pseudobulk_pairwise
Pseudobulk within	pseudobulk_within
rank_matrix	rank_matrix rank_matrix.dgCMatrix rank_matrix.matrix
sumGroups	sumGroups sumGroups.dgCMatrix sumGroups.matrix
Summarize differential gene expression pairs	summarize_dge_pairs
Get top n markers from wilcoxauc	top_markers
Get top n markers from pseudobulk DESeq2	top_markers_dds
Fast Wilcoxon rank sum test and auROC	wilcoxauc wilcoxauc.default wilcoxauc.Seurat wilcoxauc.seurat wilcoxauc.SingleCellExperiment
Group labels for observations in gene expression matrix	y