Package: MMUPHin 1.21.0

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_1.21.0.tar.gz
MMUPHin_1.21.0.zip(r-4.5)MMUPHin_1.21.0.zip(r-4.4)MMUPHin_1.21.0.zip(r-4.3)
MMUPHin_1.21.0.tgz(r-4.4-any)MMUPHin_1.21.0.tgz(r-4.3-any)
MMUPHin_1.21.0.tar.gz(r-4.5-noble)MMUPHin_1.21.0.tar.gz(r-4.4-noble)
MMUPHin_1.21.0.tgz(r-4.4-emscripten)MMUPHin_1.21.0.tgz(r-4.3-emscripten)
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-1.21.0(bioc 3.21)MMUPHin-1.20.0(bioc 3.20)

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

metagenomics microbiome batcheffect

4.43 score 45 scripts 409 downloads 2 mentions 4 exports 127 dependencies

Last updated 2 months agofrom:6b438ce4d6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 21 2024
R-4.5-win	NOTE	Dec 21 2024
R-4.5-linux	NOTE	Dec 21 2024
R-4.4-win	NOTE	Dec 21 2024
R-4.4-mac	NOTE	Dec 21 2024
R-4.3-win	NOTE	Dec 21 2024
R-4.3-mac	NOTE	Dec 21 2024

Exports:adjust_batch continuous_discover discrete_discover lm_meta

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

Performing meta-analyses of microbiome studies with MMUPHin

Siyuan Ma

Rendered fromMMUPHin.Rmdusingknitr::rmarkdownon Dec 21 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