Package: mia 1.15.20

Tuomas Borman

mia: Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Authors:Tuomas Borman [aut, cre], Felix G.M. Ernst [aut], Sudarshan A. Shetty [aut], Leo Lahti [aut], Yang Cao [ctb], Nathan D. Olson [ctb], Levi Waldron [ctb], Marcel Ramos [ctb], Héctor Corrada Bravo [ctb], Jayaram Kancherla [ctb], Domenick Braccia [ctb], Basil Courbayre [ctb], Muluh Muluh [ctb], Giulio Benedetti [ctb], Moritz Emanuel Beber [ctb], Nitesh Turaga [ctb], Chouaib Benchraka [ctb], Akewak Jeba [ctb], Himmi Lindgren [ctb], Noah De Gunst [ctb], Théotime Pralas [ctb], Shadman Ishraq [ctb], Eineje Ameh [ctb], Artur Sannikov [ctb], Hervé Pagès [ctb], Rajesh Shigdel [ctb], Katariina Pärnänen [ctb], Pande Erawijantari [ctb], Danielle Callan [ctb]

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NEWS

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

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

Datasets:
  • GlobalPatterns - Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
  • HintikkaXOData - Multiomics dataset from 40 rat samples
  • Tengeler2020 - Gut microbiota profiles of 27 individuals with ADHD and healthy controls
  • Tito2024QMP - Fecal microbiota samples from 589 patients across different colorectal cancer stages
  • dmn_se - Twins' microbiome data from 278 individuals
  • enterotype - Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing
  • esophagus - Human esophageal community from 3 individuals
  • peerj13075 - Skin microbial profiles 58 genetically unrelated individuals

On BioConductor:mia-1.15.6(bioc 3.21)mia-1.14.0(bioc 3.20)

microbiomesoftwaredataimportanalysisbioconductor

11.41 score 52 stars 4 packages 316 scripts 2.6k downloads 1 mentions 170 exports 155 dependencies

Last updated 19 days agofrom:0651f11e7f. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winNOTEJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxNOTEJan 29 2025
R-4.4-winNOTEJan 29 2025
R-4.4-macNOTEJan 29 2025
R-4.3-winNOTEJan 29 2025
R-4.3-macNOTEJan 29 2025

Exports:addAbundanceClassaddAlphaaddCCAaddClusteraddContaminantQCaddDissimilarityaddDivergenceaddDominantaddDPCoAaddHierarchyTreeaddLDAaddMediationaddNMDSaddNMFaddNotContaminantQCaddPERMANOVAaddPerSampleDominantFeaturesaddPerSampleDominantTaxaaddPrevalenceaddRDAaddTaxonomyTreeagglomerateByPrevalenceagglomerateByRankagglomerateByRanksagglomerateByVariablebestDMNFitcalculateCCAcalculateDMNcalculateDMNgroupcalculateDPCoAcalculateJSDcalculateNMDScalculateOverlapcalculateRDAcalculateUnifraccheckTaxonomyclusterconvertFromBIOMconvertFromDADA2convertFromPhyloseqconvertToBIOMconvertToPhyloseqcountDominantFeaturescountDominantTaxaestimateDivergenceestimateDiversityestimateDominanceestimateEvennessestimateFaithestimateRichnessfull_joingetAbundanceClassgetAbundantgetAlphagetBestDMNFitgetCCAgetConditionallyLowAbundantgetCrossAssociationgetDissimilaritygetDivergencegetDMNgetDominantgetDPCoAgetExperimentCrossAssociationgetExperimentCrossCorrelationgetHierarchyTreegetLDAgetLowAbundantgetMediationgetNMDSgetNMFgetPermanentlyLowAbundantgetPERMANOVAgetPrevalencegetPrevalentgetPrevalentAbundancegetPrevalentFeaturesgetPrevalentTaxagetRaregetRareFeaturesgetRareTaxagetRDAgetTaxonomyLabelsgetTaxonomyRanksgetTopgetTopFeaturesgetTopTaxagetUniquegetUniqueFeaturesgetUniqueTaxaIdTaxaToDataFrameimportBIOMimportHUMAnNimportMetaPhlAnimportMothurimportQIIME2importQZAimportTaxpastainner_joinisContaminantisNotContaminantleft_joinloadFromBiomloadFromHumannloadFromMetaphlanloadFromMothurloadFromQIIME2makePhyloseqFromTreeSEmakePhyloseqFromTreeSummarizedExperimentmakeTreeSEFromBiommakeTreeSEFromDADA2makeTreeSEFromPhyloseqmakeTreeSummarizedExperimentFromBiommakeTreeSummarizedExperimentFromDADA2makeTreeSummarizedExperimentFromPhyloseqmapTaxonomymeltAssaymeltSEmergeColsmergeFeaturesmergeFeaturesByPrevalencemergeFeaturesByRankmergeRowsmergeSamplesmergeSEsperformDMNgroupCVperSampleDominantFeaturesperSampleDominantTaxaplotNMDSrarefyAssayreadQZArelabundancerelabundance<-relAbundanceCountsright_joinrunCCArunDMNrunDPCoArunJSDrunNMDSrunOverlaprunRDArunUnifracsetTaxonomyRankssplitByRankssplitOnsubsampleCountssubsetByPrevalentsubsetByPrevalentFeaturessubsetByPrevalentTaxasubsetByRaresubsetByRareFeaturessubsetByRareTaxasubsetFeaturessubsetSamplessubsetTaxasummarizeDominancesummarytaxonomyRankEmptytaxonomyRankstaxonomyTreetestExperimentCrossAssociationtestExperimentCrossCorrelationtransformAssaytransformCountstransformFeaturestransformSamplesunsplitByRanksunsplitOnZTransform

Dependencies:abindapeaskpassassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blusterCairocellrangerclicliprclustercodetoolscolorspacecommonmarkcpp11crayoncurlDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngemmeansestimabilityfansifarverfillpatternFNNformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggnewscaleggplot2ggrastrggrepelggtextgluegridExtragridtextgtablehmshttrigraphIRangesirlbaisobandjpegjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmgcvmimeMultiAssayExperimentmunsellmvtnormnlmenumDerivopensslparallellypatchworkpermutepheatmappillarpkgconfigplyrpngprettyunitsprogresspurrrR6raggrbiomRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressreadrreadxlrematchreshape2rlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleSingleCellExperimentsitmoslamsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimenttzdbUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitevroomwithrxfunxml2XVectoryulab.utils

mia: Microbiome analysis tools

Rendered frommia.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2025-01-16
Started: 2020-10-18

Readme and manuals

Help Manual

Help pageTopics
'mia' Package.mia-package mia
Estimate alpha diversity indicesaddAlpha addAlpha,SummarizedExperiment-method getAlpha getAlpha,SummarizedExperiment-method
Clustering wrapperaddCluster addCluster,SummarizedExperiment-method
decontam functionsaddContaminantQC addContaminantQC,SummarizedExperiment-method addNotContaminantQC addNotContaminantQC,SummarizedExperiment-method isContaminant isContaminant,SummarizedExperiment-method isNotContaminant,SummarizedExperiment-method
Calculate dissimilaritiesaddDissimilarity addDissimilarity,SummarizedExperiment-method getDissimilarity getDissimilarity,ANY-method getDissimilarity,SummarizedExperiment-method getDissimilarity,TreeSummarizedExperiment-method
Estimate divergenceaddDivergence addDivergence,SummarizedExperiment-method getDivergence getDivergence,SummarizedExperiment-method
Perform mediation analysisaddMediation addMediation,SummarizedExperiment-method getMediation getMediation,SummarizedExperiment-method
Agglomerate data based on population prevalenceagglomerateByPrevalence agglomerateByPrevalence,SummarizedExperiment-method agglomerateByPrevalence,TreeSummarizedExperiment-method
Agglomerate data using taxonomic information or other groupingagglomerate-methods agglomerateByRank agglomerateByRank,SingleCellExperiment-method agglomerateByRank,SummarizedExperiment-method agglomerateByRank,TreeSummarizedExperiment-method agglomerateByRanks agglomerateByRanks,SingleCellExperiment-method agglomerateByRanks,SummarizedExperiment-method agglomerateByRanks,TreeSummarizedExperiment-method agglomerateByVariable agglomerateByVariable,SummarizedExperiment-method agglomerateByVariable,TreeSummarizedExperiment-method splitByRanks unsplitByRanks unsplitByRanks,SingleCellExperiment-method unsplitByRanks,TreeSummarizedExperiment-method
Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome DatabestDMNFit bestDMNFit,SummarizedExperiment-method calculateDMN calculateDMN,ANY-method calculateDMN,SummarizedExperiment-method calculateDMNgroup calculateDMNgroup,ANY-method calculateDMNgroup,SummarizedExperiment-method getBestDMNFit getBestDMNFit,SummarizedExperiment-method getDMN getDMN,SummarizedExperiment-method performDMNgroupCV performDMNgroupCV,ANY-method performDMNgroupCV,SummarizedExperiment-method runDMN
Create a 'TreeSummarizedExperiment' object from 'DADA2' resultsconvertFromDADA2
Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' resultsconvertFromBIOM convertToBIOM convertToBIOM,SummarizedExperiment-method importBIOM
Create a 'TreeSummarizedExperiment' object from a phyloseq objectconvertFromPhyloseq convertToPhyloseq convertToPhyloseq,SummarizedExperiment-method convertToPhyloseq,TreeSummarizedExperiment-method
These functions will be deprecated. Please use other functions instead.addPerSampleDominantFeatures addPerSampleDominantFeatures,SummarizedExperiment-method addPerSampleDominantTaxa addPerSampleDominantTaxa,SummarizedExperiment-method addTaxonomyTree addTaxonomyTree,SummarizedExperiment-method calculateJSD calculateJSD,ANY-method calculateOverlap calculateOverlap,ANY-method calculateUnifrac calculateUnifrac,ANY-method cluster cluster,SummarizedExperiment-method countDominantFeatures countDominantFeatures,SummarizedExperiment-method countDominantTaxa countDominantTaxa,SummarizedExperiment-method deprecate estimateDivergence estimateDivergence,SummarizedExperiment-method estimateDiversity estimateDiversity,ANY-method estimateDominance estimateDominance,ANY-method estimateEvenness estimateEvenness,ANY-method estimateFaith estimateFaith,ANY-method estimateRichness estimateRichness,ANY-method full_join full_join,ANY-method getExperimentCrossAssociation getExperimentCrossAssociation,MultiAssayExperiment-method getExperimentCrossAssociation,SummarizedExperiment-method getExperimentCrossCorrelation getExperimentCrossCorrelation,ANY-method getPrevalentFeatures getPrevalentFeatures,ANY-method getPrevalentFeatures,SummarizedExperiment-method getPrevalentTaxa getPrevalentTaxa,ANY-method getPrevalentTaxa,SummarizedExperiment-method getRareFeatures getRareFeatures,ANY-method getRareFeatures,SummarizedExperiment-method getRareTaxa getRareTaxa,ANY-method getRareTaxa,SummarizedExperiment-method getTopFeatures getTopFeatures,SummarizedExperiment-method getTopTaxa getTopTaxa,SummarizedExperiment-method getUniqueFeatures getUniqueFeatures,SummarizedExperiment-method getUniqueTaxa getUniqueTaxa,SummarizedExperiment-method inner_join inner_join,ANY-method left_join left_join,ANY-method loadFromBiom loadFromHumann loadFromMetaphlan loadFromMothur loadFromQIIME2 makePhyloseqFromTreeSE makePhyloseqFromTreeSE,SummarizedExperiment-method makePhyloseqFromTreeSE,TreeSummarizedExperiment-method makePhyloseqFromTreeSummarizedExperiment makePhyloseqFromTreeSummarizedExperiment,ANY-method makeTreeSEFromBiom makeTreeSEFromDADA2 makeTreeSEFromPhyloseq makeTreeSummarizedExperimentFromBiom makeTreeSummarizedExperimentFromDADA2 makeTreeSummarizedExperimentFromPhyloseq makeTreeSummarizedExperimentFromPhyloseq,ANY-method meltAssay meltAssay,SummarizedExperiment-method mergeCols mergeCols,SummarizedExperiment-method mergeCols,TreeSummarizedExperiment-method mergeFeatures mergeFeatures,SummarizedExperiment-method mergeFeatures,TreeSummarizedExperiment-method mergeFeaturesByPrevalence mergeFeaturesByPrevalence,SummarizedExperiment-method mergeFeaturesByRank mergeFeaturesByRank,SingleCellExperiment-method mergeFeaturesByRank,SummarizedExperiment-method mergeFeaturesByRank,TreeSummarizedExperiment-method mergeRows mergeRows,SummarizedExperiment-method mergeRows,TreeSummarizedExperiment-method mergeSamples mergeSamples,SummarizedExperiment-method mergeSamples,TreeSummarizedExperiment-method perSampleDominantFeatures perSampleDominantFeatures,SummarizedExperiment-method perSampleDominantTaxa perSampleDominantTaxa,SummarizedExperiment-method plotNMDS readQZA relabundance relabundance,SummarizedExperiment-method relabundance<- relabundance<-,SummarizedExperiment-method relAbundanceCounts relAbundanceCounts,SummarizedExperiment-method right_join right_join,ANY-method runJSD runJSD,SummarizedExperiment-method runOverlap runOverlap,SummarizedExperiment-method runUnifrac subsampleCounts subsampleCounts,SummarizedExperiment-method subsetByPrevalentFeatures subsetByPrevalentFeatures,ANY-method subsetByPrevalentTaxa subsetByPrevalentTaxa,ANY-method subsetByRareFeatures subsetByRareFeatures,ANY-method subsetByRareTaxa subsetByRareTaxa,ANY-method subsetFeatures subsetFeatures,SummarizedExperiment-method subsetSamples subsetSamples,SummarizedExperiment-method subsetTaxa subsetTaxa,SummarizedExperiment-method taxonomyTree taxonomyTree,SummarizedExperiment-method testExperimentCrossAssociation testExperimentCrossAssociation,ANY-method testExperimentCrossCorrelation testExperimentCrossCorrelation,ANY-method transformCounts transformFeatures transformFeatures,SummarizedExperiment-method transformSamples transformSamples,SummarizedExperiment-method ZTransform ZTransform,SummarizedExperiment-method
Twins' microbiome data from 278 individualsdmn_se twins
Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencingenterotype
Human esophageal community from 3 individualsesophagus
Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.addAbundanceClass addAbundanceClass,SingleCellExperiment-method addAbundanceClass,SummarizedExperiment-method getAbundanceClass getAbundanceClass,ANY-method getAbundanceClass,SingleCellExperiment-method getAbundanceClass,SummarizedExperiment-method getAbundant getAbundant,ANY-method getAbundant,SingleCellExperiment-method getAbundant,SummarizedExperiment-method getConditionallyLowAbundant getConditionallyLowAbundant,ANY-method getConditionallyLowAbundant,SingleCellExperiment-method getConditionallyLowAbundant,SummarizedExperiment-method getLowAbundant getLowAbundant,ANY-method getLowAbundant,SingleCellExperiment-method getLowAbundant,SummarizedExperiment-method getPermanentlyLowAbundant getPermanentlyLowAbundant,ANY-method getPermanentlyLowAbundant,SingleCellExperiment-method getPermanentlyLowAbundant,SummarizedExperiment-method
Canonical Correspondence Analysis and Redundancy AnalysisaddCCA addCCA,SingleCellExperiment-method addRDA addRDA,SingleCellExperiment-method calculateCCA calculateRDA getCCA getCCA,ANY-method getCCA,SummarizedExperiment-method getRDA getRDA,ANY-method getRDA,SummarizedExperiment-method runCCA runRDA
Calculate correlations between features of two experiments.getCrossAssociation getCrossAssociation,MultiAssayExperiment-method getCrossAssociation,SummarizedExperiment-method
Get dominant taxaaddDominant addDominant,SummarizedExperiment-method getDominant getDominant,SummarizedExperiment-method
Calculation of Double Principal Correspondance analysisaddDPCoA calculateDPCoA getDPCoA getDPCoA,ANY,ANY-method getDPCoA,TreeSummarizedExperiment,missing-method runDPCoA
Calculate hierarchy treeaddHierarchyTree addHierarchyTree,SummarizedExperiment-method getHierarchyTree getHierarchyTree,SummarizedExperiment-method hierarchy-tree
Latent Dirichlet AllocationaddLDA addLDA,SummarizedExperiment-method getLDA getLDA,SummarizedExperiment-method
Perform non-metric MDS on sample-level dataaddNMDS calculateNMDS getNMDS getNMDS,ANY-method getNMDS,SingleCellExperiment-method getNMDS,SummarizedExperiment-method runNMDS
Non-negative Matrix FactorizationaddNMF addNMF,SummarizedExperiment-method getNMF getNMF,SummarizedExperiment-method
Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)addPERMANOVA addPERMANOVA,SummarizedExperiment-method getPERMANOVA getPERMANOVA,ANY-method getPERMANOVA,SingleCellExperiment-method getPERMANOVA,SummarizedExperiment-method
Calculation prevalence information for features across samplesaddPrevalence addPrevalence,SummarizedExperiment-method getPrevalence getPrevalence,ANY-method getPrevalence,SummarizedExperiment-method getPrevalent getPrevalent,ANY-method getPrevalent,SummarizedExperiment-method getPrevalentAbundance getPrevalentAbundance,ANY-method getPrevalentAbundance,SummarizedExperiment-method getRare getRare,ANY-method getRare,SummarizedExperiment-method subsetByPrevalent subsetByPrevalent,SummarizedExperiment-method subsetByPrevalent,TreeSummarizedExperiment-method subsetByRare subsetByRare,SummarizedExperiment-method subsetByRare,TreeSummarizedExperiment-method
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.GlobalPatterns
Multiomics dataset from 40 rat samplesHintikkaXOData
Import HUMAnN results to 'TreeSummarizedExperiment'importHUMAnN
Import Metaphlan results to 'TreeSummarizedExperiment'importMetaPhlAn
Import Mothur results as a 'TreeSummarizedExperiment'importMothur
Import QIIME2 results to 'TreeSummarizedExperiment'importQIIME2 importQZA
Import taxpasta-specific BIOM results to 'TreeSummarizedExperiment'importTaxpasta
Converting a 'SummarizedExperiment' object into a long data.framemeltSE meltSE,SummarizedExperiment-method
Merge SE objects into single SE object.mergeSEs mergeSEs,list-method mergeSEs,SimpleList-method mergeSEs,SummarizedExperiment-method
mia datasetsmia-datasets
Skin microbial profiles 58 genetically unrelated individualspeerj13075
Subsample CountsrarefyAssay rarefyAssay,SummarizedExperiment-method
Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variablesplitOn splitOn,SingleCellExperiment-method splitOn,SummarizedExperiment-method splitOn,TreeSummarizedExperiment-method unsplitOn unsplitOn,list-method unsplitOn,SimpleList-method unsplitOn,SingleCellExperiment-method
Summarizing microbiome datagetTop getTop,SummarizedExperiment-method getUnique getUnique,SummarizedExperiment-method summarizeDominance summarizeDominance,SummarizedExperiment-method summary summary,SummarizedExperiment-method
Functions for accessing taxonomic data stored in 'rowData'.checkTaxonomy checkTaxonomy,SummarizedExperiment-method getTaxonomyLabels getTaxonomyLabels,SummarizedExperiment-method getTaxonomyRanks IdTaxaToDataFrame mapTaxonomy mapTaxonomy,SummarizedExperiment-method setTaxonomyRanks taxonomy-methods taxonomyRankEmpty taxonomyRankEmpty,SummarizedExperiment-method taxonomyRanks taxonomyRanks,SummarizedExperiment-method
Gut microbiota profiles of 27 individuals with ADHD and healthy controlsTengeler2020
Fecal microbiota samples from 589 patients across different colorectal cancer stagesTito2024QMP
Transform assaytransformAssay transformAssay,SingleCellExperiment-method transformAssay,SummarizedExperiment-method