Package: microbiome 1.29.0

Leo Lahti

microbiome: Microbiome Analytics

Utilities for microbiome analysis.

Authors:Leo Lahti [aut, cre], Sudarshan Shetty [aut]

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microbiome.pdf |microbiome.html✨
microbiome/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:microbiome-1.29.0(bioc 3.21)microbiome-1.28.0(bioc 3.20)

metagenomicsmicrobiomesequencingsystemsbiologyhitchiphitchip-atlashuman-microbiomemicrobiologymicrobiome-analysisphyloseqpopulation-study

12.49 score 289 stars 5 packages 1.8k scripts 2.6k downloads 114 mentions 77 exports 84 dependencies

Last updated 2 months agofrom:be82090564. Checks:OK: 2 NOTE: 3 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macERRORDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macERRORDec 19 2024

Exports:abundancesadd_besthitadd_refseqaggregate_rareaggregate_taxaalphaassociatebaselinebimodalityboxplot_abundanceboxplot_alphacollapse_replicatescombine_otu_taxcorecore_abundancecore_memberscoveragedefault_colorsdivergencediversitydominancedominantevennessgktaugroup_agegroup_bmiheathotplotinequalityintermediate_stabilityis_compositionallog_modulo_skewnesslow_abundancemap_levelsmerge_taxa2metamultimodalityneatneatsortotu_tibbleoverlapplot_atlasplot_compositionplot_coreplot_densityplot_frequenciesplot_landscapeplot_regressionplot_taxa_prevalenceplot_tippingpotential_analysisprevalencepsmelt2quietrarerare_abundancerare_membersrarityread_biom2phyloseqread_csv2phyloseqread_mothur2phyloseqread_phyloseqreadcountremove_samplesremove_taxarichnesssample_tibblespreadplotsummarize_phyloseqtax_tibbletaxatime_normalizetime_sorttimesplittoptop_taxatransform

Dependencies:ade4apeaskpassbayesmBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscolorspacecompositionscpp11crayoncurldata.tableDEoptimRdigestdplyrfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpurrrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangrobustbaseRtsneS4VectorsscalesspstringistringrsurvivalsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc

Introduction to the microbiome R package

Leo Lahti, Sudarshan Shetty, et al.

Rendered fromvignette.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2022-04-22
Started: 2013-11-20

Readme and manuals

Help Manual

Help pageTopics
R package for microbiome studiesmicrobiome-package microbiome
Abundance Matrix from Phyloseqab, abundances otu
Adds 'best_hist' to a 'phyloseq-class' Objectadd_besthit
Add 'refseq' Slot for 'dada2' based 'phyloseq' Objectadd_refseq
Aggregate Rare Groupsaggregate_rare
Aggregate Taxaaggregate_taxa
Global Ecosystem State Variablesalpha
Cross Correlation Wrapperassociate cross_correlate
HITChip Atlas with 1006 Western Adultsatlas1006
Pick Baseline Timepoint Samplesbaseline
Bimodality Analysisbimodality
Sarle's Bimodality Coefficientbimodality_sarle
Abundance Boxplotboxplot_abundance
Alpha Boxplotboxplot_alpha
Convert Correlation Matrix into a Tablecmat2table
Collapse Replicate Samplescollapse_replicates
Core Microbiotacore filter_prevalent
Core Abundancecore_abundance
Core Heatmapcore_heatmap
Core Matrixcore_matrix
Core Taxacore_members prevalent_taxa
Coverage Indexcoverage
Default Colorsdefault_colors
Density Plotdensityplot
Diet Swap Datadietswap
Divergence within a Sample Groupdivergence
Diversity Indexdiversity
Dominance Indexdominance
Dominant taxadominant
Evenness Indexevenness
Find Optimafind_optima
gktaugktau
Age Classesgroup_age
Body-Mass Index (BMI) Classesgroup_bmi
Association Heatmapheat
HITChip Taxonomyhitchip.taxonomy
Univariate Bimodality Plothotplot
Gini Indexinequality
Intermediate Stabilityintermediate_stability
Test Compositionalityis_compositional
Log-Modulo Skewness Rarity Indexlog_modulo_skewness
Low Abundance Indexlow_abundance
Map Taxonomic Levelsmap_levels
Merge Taxamerge_taxa2
Retrieve Phyloseq Metadata as Data Framemeta
Multimodality Scoremultimodality
Neatmap Sortingneat
Neatmap Sortingneatsort
Overlap Measureoverlap
Probiotics Intervention Datapeerj32
Visualize Samples of a Microbiota Atlasplot_atlas
Taxonomic Composition Plotplot_composition
Visualize OTU Coreplot_core
Plot Densityplot_density
Plot Frequenciesplot_frequencies
Landscape Plotplot_landscape
Visually Weighted Regression Plotplot_regression
Visualize Prevalence Distributions for Taxaplot_taxa_prevalence
Variation Line Plotplot_tipping
Bootstrapped Potential Analysispotential_analysis
Potential Analysis for Univariate Datapotential_univariate
OTU Prevalenceprevalence
Convert 'phyloseq-class' object to long data formatpsmelt2
Rare Microbiotarare
Rare (Non-Core) Abundance Indexrare_abundance
Rare Taxarare_members
Rarity Indexrarity
Read BIOM File into a Phyloseq Objectread_biom2phyloseq
Read Simple OTU Tables into a Phyloseq Objectread_csv2phyloseq
Read Mothur Output into a Phyloseq Objectread_mothur2phyloseq
Import phyloseq Dataread_phyloseq
Total Read Countreadcount
Exclude Samplesremove_samples
Exclude Taxaremove_taxa
Richness Indexrichness
Abundance Spread Plotspreadplot
Summarize phyloseq objectsummarize_phyloseq
Taxa Namestaxa
Utilities For 'phyloseq-class' Slots to Tibblescombine_otu_tax otu_tibble sample_tibble tax_tibble TibbleUtilites
Normalize Phyloseq Metadata Time Fieldtime_normalize
Temporal Sorting Within Subjectstime_sort
Time Splittimesplit
Identify Top Entriestop
Top Taxatop_taxa
Data Transformations for phyloseq Objectstransform