Package: GUniFrac 1.8

Jun Chen

GUniFrac: Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Authors:Jun Chen, Xianyang Zhang, Lu Yang, Lujun Zhang

GUniFrac_1.8.tar.gz
GUniFrac_1.8.tar.gz(r-4.5-noble)GUniFrac_1.8.tar.gz(r-4.4-noble)
GUniFrac_1.8.tgz(r-4.4-emscripten)GUniFrac_1.8.tgz(r-4.3-emscripten)
GUniFrac.pdf |GUniFrac.html✨
GUniFrac/json (API)

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

Peer review:

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.84 score 7 packages 196 scripts 1.7k downloads 91 mentions 14 exports 54 dependencies

Last updated 1 years agofrom:9f91b92650. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-linux-x86_64NOTEOct 25 2024

Exports:adonis3dICCdICC.SE.asymptdICC.SE.btdmanovaGMPRGUniFracPermanovaGPermanovaG2RarefySimulateMSeqSimulateMSeqCZicoSeqZicoSeq.plot

Dependencies:apecliclueclustercodetoolscolorspacedigestdirmultfansifarverfBasicsforeachggplot2ggrepelgluegssgtableinlineisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmodeestmunsellnlmepermutepillarpkgconfigR6RColorBrewerRcpprlangrmutilrpartscalesspatialstablestablediststatipstatmodtibbletimeDatetimeSeriesutf8vctrsveganviridisLitewithr

Performing differential abundance analysis using ZicoSeq

Rendered fromZicoSeq.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-09-14
Started: 2022-04-05

Readme and manuals

Help Manual

Help pageTopics
Permutational Multivariate Analysis of Variance Using Distance Matrices (Freedman-Lane permutation)adonis3
Distance-based Intra-Class Correlation CoefficientdICC
Asymptotic Standard Error of Distance-based Intra-Class Correlation CoefficientdICC.SE.asympt
Bootstrap Standard Error of Distance-based Intra-Class Correlation CoefficientdICC.SE.bt
Distance-based Multivariate Analysis of Variance (Analytical P-value Calculation)dmanova
Geometric Mean of Pairwise Ratios (GMPR) Normalization for Zero-inflated Count DataGMPR
Generalized UniFrac distances for comparing microbial communities.GUniFrac
Permutational Multivariate Analysis of Variance Using Multiple Distance MatricesPermanovaG
Permutational Multivariate Analysis of Variance Using Multiple Distance Matrices(Freedman-Lane Permutation)PermanovaG2
Rarefy a Count Table to Equal Sequencing DepthRarefy
A Semiparametric Model-based Microbiome Sequencing Data Simulator for Cross-sectional and Case-control StudiesSimulateMSeq
A Semiparametric Model-based Microbiome Sequencing Data Simulator for Longitudinal, Matched-pair, and Replicate Sampling DesignsSimulateMSeqC
Stool Microbiome OTU Count Tablestool.otu.tab
Throat Microbiome Meta Datathroat.meta
Throat Microbiome OTU Count Tablethroat.otu.tab
UPGMA Tree of Throat Microbiome OTUsthroat.tree
Vaginal Microbiome OTU Count Tablevaginal.otu.tab
A linear Model-based Permutation Test for Differential Abundance Analysis of Microbiome Data and Other Omics DataZicoSeq
A Plot Function for Visualizing the ZicoSeq ResultsZicoSeq.plot