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
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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'))

Peer review:

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.

metagenomicsmicrobiomebatcheffect

4.44 score 46 scripts 409 downloads 2 mentions 4 exports 127 dependencies

Last updated 23 days agofrom:6b438ce4d6. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winNOTENov 21 2024
R-4.5-linuxNOTENov 21 2024
R-4.4-winNOTENov 21 2024
R-4.4-macNOTENov 21 2024
R-4.3-winNOTENov 21 2024
R-4.3-macNOTENov 21 2024

Exports:adjust_batchcontinuous_discoverdiscrete_discoverlm_meta

Dependencies:abindbackportsbiglmBiobaseBiocGenericsbitopsbootbroomcarcarDatacaToolschemometricsclasscliclustercodacodetoolscolorspacecowplotcplmcpp11data.tableDBIDEoptimRDerivdiptestdoBydplyre1071edgeRfansifarverflexmixforeachFormulafpcgenericsgetoptggplot2glmmTMBglmnetgluegplotsgtablegtoolshashigraphisobanditeratorskernlabKernSmoothlabelinglarslatticelifecyclelimmalme4lmerTestlocfitloggingMaaslin2magrittrMASSmathjaxrMatrixMatrixModelsmatrixStatsmclustmetadatmetaformetagenomeSeqmgcvmicrobenchmarkminqamodelrmodeltoolsmunsellmvtnormnlmenloptrnnetnumDerivoptparsepbapplypbkrtestpcaPPpermutepheatmappillarpkgconfigplsplyrprabclusproxypsclpurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rlangrobustbaserpartscalesshapesomSparseMstatmodstringistringrsurvivaltibbletidyrtidyselectTMBtweedieutf8vctrsveganviridisLitewithrWrench

Performing meta-analyses of microbiome studies with MMUPHin

Siyuan Ma

Rendered fromMMUPHin.Rmdusingknitr::rmarkdownon Nov 21 2024.

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