Package: MicrobiomeR 0.8.0

Shaurita Hutchins

MicrobiomeR: Analyze Microbiome Data

An R package for microbiome analysis combining functions from phyloseq, metacodeR, and microbiome into an easy to use and full featured microbiome analysis package.

Authors:Robert Gilmore [aut, cre], Shaurita Hutchins [aut]

MicrobiomeR_0.8.0.tar.gz
MicrobiomeR_0.8.0.zip(r-4.7-any)MicrobiomeR_0.8.0.zip(r-4.6-any)MicrobiomeR_0.8.0.zip(r-4.5-any)
MicrobiomeR_0.8.0.tgz(r-4.6-any)MicrobiomeR_0.8.0.tgz(r-4.5-any)
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MicrobiomeR_0.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MicrobiomeR/json (API)

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

Bug tracker:https://github.com/vallenderlab/microbiomer/issues

Pkgdown/docs site:https://vallenderlab.github.io

Datasets:

On CRAN:

Conda:

metagenomicsmicrobiomesequencingsystemsbiologyalpha-diversitybeta-diversitybioinformaticscolor-palettecomprehensivemetacodermicrobial-genomicsmicrobiologymicrobiome-analysispcoapermanovaphyloseqvisualization

5.90 score 24 stars 94 scripts 59 exports 212 dependencies

Last updated from:951564731f. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develNOTE373
source / vignettesOK397
linux-releaseNOTE371
macos-releaseNOTE230
macos-oldrelNOTE251
windows-develNOTE324
windows-releaseNOTE319
windows-oldrelNOTE227
wasm-releaseOK253

Exports:%>%agglomerate_taxmapalpha_diversity_measuresalpha_diversity_plotas_analyzed_formatas_basic_formatas_custom_formatas_MicrobiomeR_formatas_phyloseq_formatas_raw_formatcombination_palettecorrelation_datacorrelation_plotcorrelation_plotscov_filtercreate_phyloseqcreate_pub_tablecreate_taxmapget_color_paletteheat_tree_parametersheat_tree_plotsis_analyzed_formatis_basic_formatis_phyloseq_formatis_raw_formatmetacoder_comp_func_1order_metacoder_dataordination_plotordination_plotsotu_id_filterotu_prevalence_filterotu_proportion_filteroutput_dirparse_taxonomy_silva_128permanovapick_new_outgrouproot_by_longest_edgeroot_phyloseq_treesample_id_filtersave_alpha_diversity_plotssave_correlation_plotssave_heat_tree_plotssave_ordination_plotssave_stacked_barplotssave_top_coefficients_barplotscico_palettestacked_barplotstacked_barplotstaxa_prevalence_filtertaxon_id_filtertop_coefficients_barplottransformertransposertreatment_matrixvalidate_MicrobiomeR_formatviridis_magma_paletteviridis_palettevlookupwhich_format

Dependencies:abindade4apeaskpassbackportsbase64encbayesmBiobaseBiocGenericsbiomformatBiostringsbitbit64bitopsbootbroombslibcachemcarcarDataclassclassIntclicliprclustercodetoolscolorspacecommonmarkcompositionscorrplotcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIDEoptimRDerivdigestdiptestdoBydplyrDTe1071evaluatefarverfastmapfastmatchfontawesomeforcatsforeachforecastFormulafracdifffsGAgenericsggfittextggplot2ggpubrggrepelggsciggsignifggthemesgluegridExtragridtextgtablehighrhmshtmltoolshtmlwidgetshttpcodehttrigraphIRangesisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetacodermgcvmicrobiomemimeminqamodelrmulttestnatservnlmenloptrnnetnumDerivopensslopenxlsxotelpbkrtestpermutephangornphyloseqpillarpixmappkgconfigplotlyplyrpngpolynomprettyunitsprogresspromisesproxypurrrquadprogquantregR6rappdirsrasterrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasrentrezreshape2ritisrlangrmarkdownrnclrobustbaserotlrredlistrstatixrstudioapiRtsnes2S4ArraysS4VectorsS7sassscalesscicosegmentedSeqinfoseqinrsfshadessolriumspSparseArraySparseMstringistringrsurvivalsystaxataxizetensorAterratibbletidyrtidyselecttimeDatetinytextriebeardtzdbunitsurcaurltoolsutf8vctrsveganviridisviridisLitevroomWikipediRwikitaxawithrwkworrmsxfunXMLxml2XVectoryamlzipzoo

About
Rendered fromabout.Rmdusingknitr::rmarkdown

Last update: 2026-09-05
Started: 2019-02-11

Data Analysis
Data Import & Wrangling | Filtering Data | Analysis | Statistical Analysis | Data Visualization | Analyzing Two "Treatment" Groups | Analyzing More than 2 "Treatment" Groups
Rendered fromanalysis.Rmdusingknitr::rmarkdown

Last update: 2026-09-05
Started: 2019-02-11

Using Color Palettes
Introduction | Getting a Color Palette | Scico | Viridis | Combining Color Palettes
Rendered fromcolor-palettes.Rmdusingknitr::rmarkdown

Last update: 2026-09-05
Started: 2019-02-11

Data Wrangling
Import | Formatting
Rendered fromdata-wrangling.Rmdusingknitr::rmarkdown

Last update: 2026-09-05
Started: 2019-02-11

Filtering Data
Data Wrangling | Taxmap Filtering | Basic Filtering | Advanced Filtering | Other Filtering | Transposing | Transforming | Excel-Like VLookup
Rendered fromfiltering.Rmdusingknitr::rmarkdown

Last update: 2026-09-05
Started: 2019-02-11

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows (Draft to JOSS)
Summary | Workflow | Utilities | Table 1: | Acknowledgments | References
Rendered frompaper.Rmdusingknitr::rmarkdown

Last update: 2019-02-27
Started: 2019-02-27

Introduction
What makes MicrobiomeR special?
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2019-02-11
Started: 2019-02-11

Readme and manuals

Help Manual

Help pageTopics
Agglomerate taxmap Objectsagglomerate_taxmap
Alpha Diversity Measuresalpha_diversity_measures
Alpha Diversity Plotalpha_diversity_plot alpha_diversity_plots
As Analyzed MicrobiomeR Formatas_analyzed_format
As Basic MicrobiomeR Formatas_basic_format
As Custom MicrobiomeR Formatas_custom_format
As MicrobiomeR Formatas_MicrobiomeR_format
As Phyloseq MicrobiomeR Formatas_phyloseq_format
As Raw MicrobiomeR Formatas_raw_format
Combine Color Palettescombination_palette
Convert Proportionsconvert_proportions
Get Correlation Plot Datacorrelation_data
Correlation Plotcorrelation_plot
Get Multiple Correlation Plotscorrelation_plots
Coefficient of Variation Filtercov_filter
Get Phyloseq Objectcreate_phyloseq
Create Publication Tablecreate_pub_table
Get Taxmap Objectcreate_taxmap
Get a Color Paletteget_color_palette
Get Heat Tree Parametersheat_tree_parameters
Get Heat Tree Plotsheat_tree_plots
Is Analyzed MicrobiomeR Formatis_analyzed_format
Is Basic MicrobiomeR Formatis_basic_format
Is Phyloseq MicrobiomeR Formatis_phyloseq_format
Is Raw MicrobiomeR Formatis_raw_format
Melt Taxmapmelt_taxmap
Metacoder Comparison Function #1metacoder_comp_func_1
The MicrobiomeR FormatsMicrobiomeR_Formats
The MicrobiomeR WorkflowMicrobiomeR_Workflow
Order Metacoder Observation Dataorder_metacoder_data
Ordination Plotordination_plot ordination_plots
Filter OTU Ids from Taxmap Objectsotu_id_filter
OTU Prevalence Filterotu_prevalence_filter
OTU Proportion Filterotu_proportion_filter
Create an Output Directoryoutput_dir
Parse elements of a taxonomy vectorparse_taxonomy_silva_128
PERMANOVApermanova
Phyloseq Data with 2 Treatment Groupsphyloseq_silva_2
Phyloseq Data with 3 Treatment Groupsphyloseq_silva_3
Pick Outgroup for Treepick_new_outgroup
Get Plot Limitsplot_limits
"raw_format" Data with 2 Treatment Groupsraw_silva_2
"raw_format" Data with 3 Treatment Groupsraw_silva_3
Root Phylogenetic Treeroot_by_longest_edge
Root phyloseq tree.root_phyloseq_tree
Filter Samples Ids from Taxmap Objectssample_id_filter
Save Alpha Diversity Plotssave_alpha_diversity_plots
Save Correlation Plotssave_correlation_plots
Save Heat Tree Plotssave_heat_tree_plots
Save Ordination Plotssave_ordination_plots
Save Stacked Barplotssave_stacked_barplots
Save Top Coefficients Barplotsave_top_coefficients_barplot
Scico Palette Functionscico_palette
Stacked Barplotstacked_barplot
Stacked Barplotsstacked_barplots
Taxonomic Prevalence Filter (Metacoder)taxa_prevalence_filter
Filter Taxon Ids from Taxmap Objectstaxon_id_filter
Top Coefficients Barplottop_coefficients_barplot
Transforming Tidy Datatransformer
Transposing Tidy Datatransposer
Get Treatment Matrixtreatment_matrix
Validate MicrobiomeR Formatvalidate_MicrobiomeR_format
Viridis-Magma Palette Functionviridis_magma_palette
Viridis Palette Functionviridis_palette
Mock Excel "VlookUp" Functionvlookup
Which MicrobiomeR Formatwhich_format