Package: MetaLonDA 1.1.8

Ahmed A. Metwally

MetaLonDA: Metagenomics Longitudinal Differential Abundance Method

Identify time intervals of differentially abundant metagenomic features in longitudinal studies (Metwally AA, et al., Microbiome, 2018 <doi:10.1186/s40168-018-0402-y>).

Authors:Ahmed A. Metwally, Yang Dai, Patricia W. Finn, David L. Perkins

MetaLonDA_1.1.8.tar.gz
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MetaLonDA.pdf |MetaLonDA.html
MetaLonDA/json (API)

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

Peer review:

Bug tracker:https://github.com/aametwally/metalonda/issues

Datasets:
  • metalonda_test_data - Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points

On CRAN:

differential-abundance-methodslongitudinal-studiesmetagenomicsmicrobiomenegative-binomial-distributionsmoothing-splines

5.75 score 16 stars 8 scripts 190 downloads 7 mentions 14 exports 87 dependencies

Last updated 5 years agofrom:263e1d33c4. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 14 2024
R-4.5-winNOTEOct 14 2024
R-4.5-linuxNOTEOct 14 2024
R-4.4-winNOTEOct 14 2024
R-4.4-macNOTEOct 14 2024
R-4.3-winNOTEOct 14 2024
R-4.3-macNOTEOct 14 2024

Exports:areaPermutationcurveFittingfindSigIntervalintervalAreametalondametalondaAllnormalizepermutationvisualizeAreavisualizeARHistogramvisualizeFeaturevisualizeFeatureSplinevisualizeTimeIntervalsvisualizeVolcanoPlot

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelbitopscaToolsclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2doParalleledgeRfansifarverforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2glmnetgluegplotsgssgtablegtoolshttrIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetagenomeSeqmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpracmaR6RColorBrewerRcppRcppArmadilloRcppEigenrlangS4ArraysS4VectorsscalesshapesnowSparseArraystatmodSummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrWrenchXVectorzlibbioczoo

An Introduction to the MetaLonDA Package

Rendered fromMetaLonDA.Rmdusingknitr::rmarkdownon Oct 14 2024.

Last update: 2019-04-13
Started: 2018-01-21