Package: microbiomeutilities 1.00.17

Sudarshan Shetty

microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

This is a supporting tool for extending the functionality of both phyloseq and microbiome R packages.

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

microbiomeutilities_1.00.17.tar.gz
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microbiomeutilities.pdf |microbiomeutilities.html✨
microbiomeutilities/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/microsud/microbiomeutilities/issues

Datasets:

On CRAN:

16sampliconcore-microbiomemetagenomicsmicrobial-communitiesmicrobiomemicrobiome-analysisqc-pipelinesequencing

6.08 score 33 stars 364 scripts 40 exports 117 dependencies

Last updated 2 years agofrom:046a9f928f. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winWARNINGNov 06 2024
R-4.5-linuxWARNINGNov 06 2024
R-4.4-winWARNINGNov 06 2024
R-4.4-macWARNINGNov 06 2024
R-4.3-winWARNINGNov 06 2024
R-4.3-macWARNINGNov 06 2024

Exports:add_refseqaggregate_top_taxa2dominant_taxafind_samples_taxaformat_to_besthitget_group_abundancesget_microbiome_dataget_tibblejoin_otu_taxlist_microbiome_datamake_pairspeak_abundancepeak_basepeak_samplepeak_taxonomypercent_classifiedphy_to_ldfplasticityplot_abund_prevplot_alpha_diversitiesplot_alpha_rcurveplot_areaplot_diversity_statsplot_listed_taxaplot_ordination_utilsplot_ordiplot_coreplot_paired_abundancesplot_read_distributionplot_select_taxaplot_spaghettiplot_taxa_boxplotplot_taxa_compositionplot_taxa_cvplot_taxa_heatmapprep_ternaryprint_pssimple_heatmaptaxa_distributiontaxa_summarytheme_biome_utils

Dependencies:abindade4apeaskpassbackportsbayesmBiobaseBiocGenericsbiomformatBiostringsbootbroomcarcarDatacliclustercodetoolscolorspacecompositionscorrplotcowplotcpp11crayoncurldata.tableDEoptimRDerivdigestdoBydplyrfansifarverforeachFormulagenericsGenomeInfoDbGenomeInfoDbDatagghalvesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmicrobiomemimeminqamodelrmulttestmunsellnlmenloptrnnetnumDerivopensslpbkrtestpermutepheatmapphyloseqpillarpixmappkgconfigplyrpolynompurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rhdf5rhdf5filtersRhdf5librlangrobustbaserstatixRtsneS4VectorsscalesspSparseMstringistringrsurvivalsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc

Introduction to microbiomeutilities

Rendered frommicrobiomeutilities.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2022-11-23
Started: 2018-04-19

Longitudinal data analysis and visualization

Rendered frommicrobiomeutilities_ts.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-01-18
Started: 2020-10-27

Readme and manuals

Help Manual

Help pageTopics
Add refseq slot for dada2 based phyloseq objectadd_refseq
Aggregate Top Taxa v2aggregate_top_taxa2
Dominant Taxadominant_taxa
Find samples dominated by specific taxafind_samples_taxa
Formatting the 'phyloseq-class' Object advancedformat_to_besthit
Taxa abundance summary by groupget_group_abundances
Download test microbiome dataget_microbiome_data
Convert Phyloseq Slots to Tibblesget_tibble
Test data 2hmp2
Join otu_table and tax_table to Tibblejoin_otu_tax
List of available datasetslist_microbiome_data
Make pairsmake_pairs
Peak into 'phyloseq' objectspeak-methods peak_abundance peak_abundance,phyloseq-method peak_base peak_base,ANY-method peak_sample peak_sample,phyloseq-method peak_taxonomy peak_taxonomy,phyloseq-method
Summarize the percent taxa classification for 'phyloseq-class'percent_classified
Convert 'phyloseq-class' object to long data formatphy_to_ldf
Plasticityplasticity
Mean Abundance-Prevalence relationplot_abund_prev
Creat a plot for alpha diversities calculated using the 'microbiome' packageplot_alpha_diversities
Rarefaction curves for alpha diversity indicesplot_alpha_rcurve
Area plotplot_area
Diversity plot with statsplot_diversity_stats
A boxplot for user specified list of taxaplot_listed_taxa
Plot species loading with ordinationsplot_ordination_utils
Plotting core microbiota on ordinationsplot_ordiplot_core
A paired-boxplot for user specified list of taxaplot_paired_abundances
Distribution of readsplot_read_distribution
A boxplot for user specified list of taxaplot_select_taxa
Spaghetti Plotsplot_spaghetti
Taxonomic Composition Plot boxplotplot_taxa_boxplot
Taxonomic Composition Plotplot_taxa_composition
Coefficient of variationsplot_taxa_cv
Heatmap using 'phyloseq-class' and 'pheatmap'plot_taxa_heatmap
Create table for ternary plot OTUprep_tern_otu
Create table for Ternary plotprep_ternary
Overview of 'phyloseq-class'print_ps
Simple Heatmapsimple_heatmap
Distribution of taxataxa_distribution
Pool Taxataxa_pooler_mcola
Give taxa summary at specified taxonomic leveltaxa_summary
Custom theme for microbiomeutilities pkgtheme_biome_utils
Test datazackular2014