Package: waddR 1.21.0

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]

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waddR.pdf |waddR.html✨
waddR/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:waddR-1.21.0(bioc 3.21)waddR-1.20.0(bioc 3.20)

softwarestatisticalmethodsinglecelldifferentialexpression

6.70 score 25 stars 6 scripts 141 downloads 7 exports 94 dependencies

Last updated 23 days agofrom:fc50998785. Checks:OK: 1 NOTE: 1 ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64ERRORNov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64ERRORNov 19 2024
R-4.4-mac-x86_64ERRORNov 19 2024
R-4.4-mac-aarch64ERRORNov 19 2024
R-4.3-win-x86_64ERRORNov 19 2024
R-4.3-mac-x86_64ERRORNov 19 2024
R-4.3-mac-aarch64ERRORNov 19 2024

Exports:permutationssquared_wass_approxsquared_wass_decomptestZeroeswasserstein_metricwasserstein.scwasserstein.test

Dependencies:abindarmaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobbootcachemclicodacodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrEnvStatsevafansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptrnortestopensslpillarpkgconfigplogrpurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangRSQLiteS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

The waddR package

Rendered fromwaddR.Rmdusingknitr::rmarkdownon Nov 19 2024.

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

2-Wasserstein distance calculation

Rendered fromwasserstein_metric.Rmdusingknitr::rmarkdownon Nov 19 2024.

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

Detection of differential gene expression distributions in single-cell RNA sequencing data

Rendered fromwasserstein_singlecell.Rmdusingknitr::rmarkdownon Nov 19 2024.

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

Two-sample tests based on the 2-Wasserstein distance

Rendered fromwasserstein_test.Rmdusingknitr::rmarkdownon Nov 19 2024.

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