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'))

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)

software statisticalmethod singlecell differentialexpression cpp

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

Last updated 2 months agofrom:fc50998785. Checks:OK: 1 NOTE: 1 ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win-x86_64	ERROR	Dec 19 2024
R-4.5-linux-x86_64	NOTE	Dec 19 2024
R-4.4-win-x86_64	ERROR	Dec 19 2024
R-4.4-mac-x86_64	ERROR	Dec 19 2024
R-4.4-mac-aarch64	ERROR	Dec 19 2024
R-4.3-win-x86_64	ERROR	Dec 19 2024
R-4.3-mac-x86_64	ERROR	Dec 19 2024
R-4.3-mac-aarch64	ERROR	Dec 19 2024

Exports:permutations squared_wass_approx squared_wass_decomp testZeroes wasserstein_metric wasserstein.sc wasserstein.test

Dependencies:abind arm askpass BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob boot cachem cli coda codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray dplyr EnvStats eva fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa munsell nlme nloptr nortest openssl pillar pkgconfig plogr purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang RSQLite S4Arrays S4Vectors scales SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

The waddR package

Rendered fromwaddR.Rmdusingknitr::rmarkdownon Dec 19 2024.

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

2-Wasserstein distance calculation

Rendered fromwasserstein_metric.Rmdusingknitr::rmarkdownon Dec 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 Dec 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 Dec 19 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
waddR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance	waddR-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 test	brownianBridgeEmpcdf.url
Return permutations of a given vector as columns in a matrix	permutations
Compute approximated squared 2-Wasserstein distance	squared_wass_approx
Compute the squared 2-Wasserstein distance based on a decomposition	squared_wass_decomp
Test for differential proportions of zero gene expression	testZeroes testZeroes,matrix,vector,ANY-method testZeroes,SingleCellExperiment,SingleCellExperiment,vector-method
Calculate the p-Wasserstein distance	wasserstein_metric
Two-sample semi-parametric test for single-cell RNA-sequencing data to check for differences between two distributions using the 2-Wasserstein distance	wasserstein.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 distance	wasserstein.test