Man pages for microbiome
Microbiome Analytics

abundancesAbundance Matrix from Phyloseq
aggregate_taxaAggregate Taxa
associateCross Correlation Wrapper
atlas1006HITChip Atlas with 1006 Western Adults
baselinePick Baseline Timepoint Samples
bimodalityBimodality Analysis
bimodality_sarleSarle's Bimodality Coefficient
boxplot_abundanceAbundance Boxplot
chunk_reorderChunk Reorder
cmat2tableConvert Correlation Matrix into a Table
coreCore Microbiota
core_abundanceCore Abundance
core_heatmapCore Heatmap
core_matrixCore Matrix
core_membersCore Taxa
coverageCoverage Index
densityplotDensity Plot
dietswapDiet Swap Data
divergenceDiversity within a Sample Group
diversitiesDiversity Index
dominanceDominance Index
estimate_stabilityEstimate Stability
evennessEvenness Index
find_optimaFind Optima
globalGlobal Ecosystem State Variables
group_ageAge Classes
group_bmiBody-Mass Index (BMI) Classes
heatAssociation Heatmap
hitchip.taxonomyHITChip Taxonomy
hotplotUnivariate Bimodality Plot
inequalityGini Index
intermediate_stabilityIntermediate Stability
log_modulo_skewnessLog-Modulo Skewness Rarity Index
low_abundanceLow Abundance Index
map_levelsMap Taxonomic Levels
merge_taxa2Merge Taxa
metaRetrieve Phyloseq Metadata as Data Frame
microbiome-packageR package for microbiome studies
multimodalityMultimodality Score
neatNeatmap Sorting
neatsortNeatmap Sorting
noncore_abundanceNon-Core Abundance Index
noncore_membersSelect Non-Core Taxa
peerj32Probiotics Intervention Data
plot_atlasVisualize Samples of a Microbiota Atlas
plot_compositionTaxonomic Composition Plot
plot_coreVisualize OTU Core
plot_densityPlot Density
plot_frequenciesPlot Frequencies
plot_landscapeLandscape Plot
plot_regressionVisually Weighted Regression Plot
plot_taxa_prevalenceVisualize Prevalence Distributions for Taxa
plot_tippingVariation Line Plot
potential_analysisBootstrapped Potential Analysis
potential_univariatePotential Analysis for Univariate Data
prevalenceOTU Prevalence
quietQuiet Output
radial_thetaRadial Theta Function
rare_membersRare Taxa
rarityRarity Index
read_biom2phyloseqRead BIOM File into a Phyloseq Object
read_csv2phyloseqRead Simple OTU Tables into a Phyloseq Object
read_mothur2phyloseqRead Mothur Output into a Phyloseq Object
read_phyloseqImport phyloseq Data
remove_samplesExclude Samples
remove_taxaExclude Taxa
richnessRichness Index
summarize_phyloseqSummarize phyloseq object
taxaTaxa Names
time_normalizeNormalize Phyloseq Metadata Time Field
time_sortTemporal Sorting Within Subjects
top_taxaTop Taxa
transformData Transformations for phyloseq Objects
variable_membersVariable Microbiota
write_phyloseqExporting phyloseq Data in CSV Files
ztransformZ Transformation
microbiome documentation built on Nov. 1, 2018, 2:40 a.m.