Package: waddR 1.27.0

Julian Flesch

waddR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data.

Authors:Roman Schefzik [aut], Julian Flesch [cre]

waddR_1.27.0.tar.gz
waddR_1.27.0.zip(r-4.7-x86_64)waddR_1.27.0.zip(r-4.7-arm64)waddR_1.27.0.zip(r-4.6-x86_64)waddR_1.27.0.zip(r-4.6-arm64)
waddR_1.27.0.tgz(r-4.6-x86_64)waddR_1.27.0.tgz(r-4.6-arm64)
waddR_1.27.0.tar.gz(r-4.7-arm64)waddR_1.27.0.tar.gz(r-4.7-x86_64)waddR_1.27.0.tar.gz(r-4.6-arm64)waddR_1.27.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
waddR/json (API)

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

Bug tracker:https://github.com/goncalves-lab/waddr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:waddR-1.27.0(bioc 3.24)waddR-1.26.0(bioc 3.23)

softwarestatisticalmethodsinglecelldifferentialexpressioncpp

7.25 score 28 stars 32 scripts 284 downloads 7 exports 76 dependencies

Last updated from:a43f73c78a. Checks:7 ERROR, 4 NOTE, 1 OK, 4 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR216
linux-devel-arm64NOTE840
linux-devel-x86_64NOTE1159
source / vignettesOK363
linux-release-arm64NOTE827
linux-release-x86_64NOTE1063
macos-release-arm64ERROR269
macos-release-x86_64ERROR569
macos-oldrel-arm64FAIL81
macos-oldrel-x86_64FAIL182
windows-devel-arm64ERROR449
windows-devel-x86_64ERROR457
windows-release-arm64ERROR527
windows-release-x86_64ERROR559
windows-oldrel-x86_64FAIL83
wasm-releaseFAIL125

Exports:permutationssquared_wass_approxsquared_wass_decomptestZeroeswasserstein_metricwasserstein.scwasserstein.test

Dependencies:abindarmaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootcachemclicodacodetoolscpp11curlDBIdbplyrDelayedArraydplyrevafastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2IRangeslambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseminqanlmenloptropensslpillarpkgconfigpurrrR6rbibutilsRcppRcppArmadilloRcppEigenRdpackreformulasrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector

The waddR package
Introduction | 2-Wasserstein distance functions | Testing for differences between two distributions | Testing for differences between two distributions in the context of scRNAseq data | Installation | Session info
Rendered fromwaddR.Rmdusingknitr::rmarkdown

Last update: 2023-05-31
Started: 2019-08-06

Detection of differential gene expression distributions in single-cell RNA sequencing data
Application to an example data set | See also | Session info
Rendered fromwasserstein_singlecell.Rmdusingknitr::rmarkdown

Last update: 2020-04-06
Started: 2019-08-06

Two-sample tests based on the 2-Wasserstein distance
Testing procedures | Examples | See also | Session info
Rendered fromwasserstein_test.Rmdusingknitr::rmarkdown

Last update: 2020-04-03
Started: 2019-08-06

2-Wasserstein distance calculation
Background | Usage in two-sample setting | Three implementations | See also | Session Info
Rendered fromwasserstein_metric.Rmdusingknitr::rmarkdown

Last update: 2020-04-03
Started: 2019-08-06

Readme and manuals

Help Manual

Help pageTopics
waddR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distancewaddR-package waddR
Compute value of the asymptotic CDF occuring in the asymptotic theory-based test.brownianBridgeEmpcdf
Compute combined p-value using Fisher's method for several pairs of p-values.combinePVal
Compute combined p-value using Fisher's method.fishersCombinedPval
Compute p-value based on generalized Pareto distribution fitting.gpdFittedPValue
Compute the quantile-quantile correlation.quantileCorrelation
Compute relative error.relativeError
Check for differential distributions in single-cell RNA sequencing data via a semi-paramteric test using the 2-Wasserstein distance.testWass
Asymptotic theory-based test using the 2-Wasserstein distance to check for differential distributions.wassersteinTestAsy
Semi-parametric test using the 2-Wasserstein distance to check for differential distributions.wassersteinTestSp
Permutation procedure that calculates the squared 2-Wasserstein distances for random shuffles of two input samples representing two conditions.wassPermProcedure
URL for downloading the asymptotic CDF occuring in the asymptotic theory-based testbrownianBridgeEmpcdf.url
Return permutations of a given vector as columns in a matrixpermutations
Compute approximated squared 2-Wasserstein distancesquared_wass_approx
Compute the squared 2-Wasserstein distance based on a decompositionsquared_wass_decomp
Test for differential proportions of zero gene expressiontestZeroes testZeroes,matrix,vector,ANY-method testZeroes,SingleCellExperiment,SingleCellExperiment,vector-method
Calculate the p-Wasserstein distancewasserstein_metric
Two-sample semi-parametric test for single-cell RNA-sequencing data to check for differences between two distributions using the 2-Wasserstein distancewasserstein.sc wasserstein.sc,matrix,vector-method wasserstein.sc,SingleCellExperiment,SingleCellExperiment,ANY,ANY,ANY-method wasserstein.sc,SingleCellExperiment,SingleCellExperiment-method wasserstein.sc-method,matrix,vector,ANY,ANY,ANY-method
Two-sample test to check for differences between two distributions using the 2-Wasserstein distancewasserstein.test