Package: MMUPHin 1.19.1

Siyuan MA

MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.

Authors:Siyuan Ma

MMUPHin_1.19.1.tar.gz
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MMUPHin.pdf |MMUPHin.html✨
MMUPHin/json (API)
NEWS

# Install 'MMUPHin' in R:

install.packages('MMUPHin', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CRC_abd - Species level feature abundance data of five public CRC studies
CRC_meta - Sample metadata of five public CRC studies
vaginal_abd - Species level feature abundance data of two public vaginal studies
vaginal_meta - Sample metadata of two public vaginal studies

On BioConductor:MMUPHin-1.19.1(bioc 3.20)MMUPHin-1.18.1(bioc 3.19)

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

bioconductor-package

4 exports 0.91 score 137 dependencies 2 mentions

Last updated 2 months agofrom:8ddf35dfaa

Exports:adjust_batch continuous_discover discrete_discover lm_meta

Dependencies:abind backports biglm Biobase BiocGenerics bitops boot brio broom callr car carData caTools chemometrics class cli cluster coda codetools colorspace cowplot cplm cpp11 crayon data.table DBI DEoptimR desc diffobj digest diptest dplyr e1071 edgeR evaluate fansi farver flexmix foreach fpc fs generics getopt ggplot2 glmmTMB glmnet glue gplots gtable gtools hash igraph isoband iterators jsonlite kernlab KernSmooth labeling lars lattice lifecycle limma lme4 lmerTest locfit logging Maaslin2 magrittr MASS mathjaxr Matrix MatrixModels matrixStats mclust metadat metafor metagenomeSeq mgcv minqa modeltools munsell mvtnorm nlme nloptr nnet numDeriv optparse pbapply pbkrtest pcaPP permute pheatmap pillar pkgbuild pkgconfig pkgload pls plyr prabclus praise processx proxy ps pscl purrr quantreg R6 RColorBrewer Rcpp RcppEigen rematch2 reshape2 rlang robustbase rpart rprojroot scales shape som SparseM statmod stringi stringr survival testthat tibble tidyr tidyselect TMB tweedie utf8 vctrs vegan viridisLite waldo withr Wrench

Performing meta-analyses of microbiome studies with MMUPHin

Siyuan Ma

Rendered fromMMUPHin.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2024-05-19
Started: 2019-08-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Zero-inflated empirical Bayes adjustment of batch effect in compositional feature abundance data	adjust_batch
Unsupervised meta-analytical discovery and validation of continuous structures in microbial abundance data	continuous_discover
Species level feature abundance data of five public CRC studies	CRC_abd
Sample metadata of five public CRC studies	CRC_meta
Unsupervised meta-analytical discovery and validation of discrete clustering structures in microbial abundance data	discrete_discover
Covariate adjusted meta-analytical differential abundance testing	lm_meta
Species level feature abundance data of two public vaginal studies	vaginal_abd
Sample metadata of two public vaginal studies	vaginal_meta