Package: miaSim 1.13.0

Yagmur Simsek

miaSim: Microbiome Data Simulation

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

Authors:Yagmur Simsek [cre, aut], Karoline Faust [aut], Yu Gao [aut], Emma Gheysen [aut], Daniel Rios Garza [aut], Tuomas Borman [aut], Leo Lahti [aut]

miaSim_1.13.0.tar.gz
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miaSim.pdf |miaSim.html✨
miaSim/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/microbiome/miasim/issues

On BioConductor:miaSim-1.13.0(bioc 3.21)miaSim-1.12.0(bioc 3.20)

microbiomesoftwaresequencingdnaseqatacseqcoveragenetwork

6.57 score 18 stars 23 scripts 150 downloads 14 exports 71 dependencies

Last updated 2 months agofrom:667f35c367. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:.estimateAFromSimulations.eventTimes.rdirichlet.simulationTimespowerlawArandomArandomEsimulateConsumerResourcesimulateGLVsimulateHubbellsimulateHubbellRatessimulateRickersimulateSOIsimulateStochasticLogistic

Dependencies:abindapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsclicodetoolscpp11crayoncurlDelayedArraydeSolvedigestdplyrfansiformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimenlmeopensslpillarpkgconfigpoweRlawpracmapurrrR6RcpprlangS4ArraysS4VectorsSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentUCSC.utilsutf8vctrswithrXVectoryulab.utilszlibbioc

miaSim: Microbiome Data Simulation

miaSim authors

Rendered frommiaSim.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-06-02
Started: 2021-09-17