Introduction | Installation | Load the package | Divergence between time points | Types of divergence provided | Purpose | Practical application | Visualize time series | Session info
Package: miaTime 1.3.0
Tuomas Borman
miaTime: Microbiome Time Series Analysis
The `miaTime` package provides tools for microbiome time series analysis based on (Tree)SummarizedExperiment infrastructure.
Authors:
miaTime_1.3.0.tar.gz
miaTime_1.3.0.zip(r-4.7)miaTime_1.3.0.zip(r-4.6)miaTime_1.3.0.zip(r-4.5)
miaTime_1.3.0.tgz(r-4.6-any)miaTime_1.3.0.tgz(r-4.5-any)
miaTime_1.3.0.tar.gz(r-4.7-any)miaTime_1.3.0.tar.gz(r-4.6-any)
miaTime_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
miaTime/json (API)
| # Install 'miaTime' in R: |
| install.packages('miaTime', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/microbiome/miatime/issues
Datasets:
- crohn_survival - Survival microbiome data from 150 individuals with longitudinal measurements
- hitchip1006 - HITChip Atlas with 1006 Western Adults
- Kumaraswamy2024 - Kumaraswamy2024
- minimalgut - Human Gut Minimal Microbiome Profiling Data
- SilvermanAGutData - SilvermanAGutData
- temporalMicrobiome20 - Gut Microbiome Profiling 20 Belgian Women
On BioConductor:miaTime-1.3.0(bioc 3.24)miaTime-1.2.0(bioc 3.23)
Last updated from:91f4956001. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 267 | ||
| linux-devel-x86_64 | OK | 503 | ||
| source / vignettes | OK | 367 | ||
| linux-release-x86_64 | OK | 512 | ||
| macos-release-arm64 | OK | 328 | ||
| macos-oldrel-arm64 | OK | 336 | ||
| windows-devel | OK | 345 | ||
| windows-release | OK | 372 | ||
| windows-oldrel | OK | 356 | ||
| wasm-release | OK | 206 |
Exports:addBaselineDivergenceaddBimodalityaddShortTermChangeaddStabilityaddStepwiseDivergencegetBaselineDivergencegetBimodalitygetShortTermChangegetStabilitygetStepwiseDivergence
Dependencies:abindapeassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblustercliclustercodetoolscpp11crayonDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodivefarverFNNformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelgluegridExtragtableigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmiaMultiAssayExperimentnlmepermutepheatmappillarpkgconfigplyrpurrrR6rappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressreshape2rlangRSpectrarsvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimenttibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8uwotvctrsveganviporviridisviridisLitewithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'miaTime' Package. | miaTime-package miaTime |
| Short term changes in abundance | addShortTermChange addShortTermChange,SummarizedExperiment-method getShortTermChange getShortTermChange,SummarizedExperiment-method |
| Survival microbiome data from 150 individuals with longitudinal measurements | crohn_survival |
| Beta diversity between the baseline and later time steps | addBaselineDivergence addBaselineDivergence,SummarizedExperiment-method getBaselineDivergence getBaselineDivergence,SummarizedExperiment-method |
| Calculate coefficient of bimodality. | addBimodality addBimodality,SummarizedExperiment-method getBimodality getBimodality,SummarizedExperiment-method |
| Estimate stability | addStability addStability,SummarizedExperiment-method getStability getStability,SummarizedExperiment-method |
| Beta diversity between consecutive time steps | addStepwiseDivergence addStepwiseDivergence,SummarizedExperiment-method getStepwiseDivergence getStepwiseDivergence,ANY-method |
| HITChip Atlas with 1006 Western Adults | hitchip1006 |
| Kumaraswamy2024 | Kumaraswamy2024 |
| Human Gut Minimal Microbiome Profiling Data | minimalgut |
| SilvermanAGutData | SilvermanAGutData |
| Gut Microbiome Profiling 20 Belgian Women | temporalMicrobiome20 |