Introduction | Installation | Load the package | Divergence between time points | Types of divergence provided | Purpose | Practical application | Visualize time series | Session info
Package: miaTime 1.3.2
Tuomas Borman
miaTime: Microbiome Time Series Analysis
The `miaTime` package provides tools for microbiome time series analysis based on (Tree)SummarizedExperiment infrastructure.
Authors:
miaTime_1.3.2.tar.gz
miaTime_1.3.2.zip(r-4.7-any)miaTime_1.3.2.zip(r-4.6-any)miaTime_1.3.2.zip(r-4.5-any)
miaTime_1.3.2.tgz(r-4.6-any)miaTime_1.3.2.tgz(r-4.5-any)
miaTime_1.3.2.tar.gz(r-4.7-any)miaTime_1.3.2.tar.gz(r-4.6-any)
miaTime_1.3.2.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
- HMP_2019_ibdmdb - HMP_2019_ibdmdb
- Kumaraswamy2024 - Kumaraswamy2024
- minimalgut - Human Gut Minimal Microbiome Profiling Data
- SilvermanAGutData - SilvermanAGutData
- temporalMicrobiome20 - Gut Microbiome Profiling 20 Belgian Women
On BioConductor:miaTime-1.3.1(bioc 3.24)miaTime-1.2.0(bioc 3.23)
Last updated from:534c76d28c. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 232 | ||
| linux-devel | OK | 768 | ||
| source / vignettes | OK | 495 | ||
| linux-release | OK | 522 | ||
| macos-release | OK | 449 | ||
| macos-oldrel | OK | 313 | ||
| windows-devel | OK | 335 | ||
| windows-release | OK | 492 | ||
| windows-oldrel | OK | 369 | ||
| wasm-release | OK | 168 |
Exports:addBaselineDivergenceaddBimodalityaddShortTermChangeaddStabilityaddStepwiseDivergenceaddSurvivalgetBaselineDivergencegetBimodalitygetShortTermChangegetStabilitygetStepwiseDivergencegetSurvival
Dependencies:abindapeassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblustercliclustercodetoolscpp11crayonDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodivefarverFNNforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelglmnetgluegridExtragtableigraphIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmiaMultiAssayExperimentnlmepermutepheatmappillarpkgconfigplyrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRdpackreshape2rlangRSpectrarsvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoshapeSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8uwotvctrsveganviporviridisviridisLitewithrXVectoryulab.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 |
| Survival analysis | addSurvival addSurvival,SummarizedExperiment-method getSurvival getSurvival,SummarizedExperiment-method |
| HITChip Atlas with 1006 Western Adults | hitchip1006 |
| HMP_2019_ibdmdb | HMP_2019_ibdmdb |
| Kumaraswamy2024 | Kumaraswamy2024 |
| Human Gut Minimal Microbiome Profiling Data | minimalgut |
| SilvermanAGutData | SilvermanAGutData |
| Gut Microbiome Profiling 20 Belgian Women | temporalMicrobiome20 |