Package: microbiome 1.35.0

Leo Lahti

microbiome: Microbiome Analytics

Utilities for microbiome analysis.

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

microbiome_1.35.0.tar.gz
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microbiome_1.35.0.tgz(r-4.6-any)microbiome_1.35.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
microbiome/json (API)

# Install 'microbiome' in R:

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

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

Datasets:

atlas1006 - HITChip Atlas with 1006 Western Adults
dietswap - Diet Swap Data
hitchip.taxonomy - HITChip Taxonomy
peerj32 - Probiotics Intervention Data

On BioConductor:microbiome-1.35.0(bioc 3.24)microbiome-1.34.0(bioc 3.23)

metagenomics microbiome sequencing systemsbiology hitchip hitchip-atlas human-microbiome microbiology microbiome-analysis phyloseq population-study

12.71 score 318 stars 5 packages 3.4k scripts 114 mentions 77 exports 70 dependencies

Last updated from:b769911d78. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	185
linux-devel-x86_64	NOTE	369
source / vignettes	OK	246
linux-release-x86_64	NOTE	289
macos-release-arm64	NOTE	230
macos-oldrel-arm64	NOTE	217
windows-devel	NOTE	246
windows-release	NOTE	221
windows-oldrel	NOTE	225
wasm-release	OK	151

Exports:abundances add_besthit add_refseq aggregate_rare aggregate_taxa alpha associate baseline bimodality boxplot_abundance boxplot_alpha collapse_replicates combine_otu_tax core core_abundance core_members coverage default_colors divergence diversity dominance dominant evenness gktau group_age group_bmi heat hotplot inequality intermediate_stability is_compositional log_modulo_skewness low_abundance map_levels merge_taxa2 meta multimodality neat neatsort otu_tibble overlap plot_atlas plot_composition plot_core plot_density plot_frequencies plot_landscape plot_regression plot_taxa_prevalence plot_tipping potential_analysis prevalence psmelt2 quiet rare rare_abundance rare_members rarity read_biom2phyloseq read_csv2phyloseq read_mothur2phyloseq read_phyloseq readcount remove_samples remove_taxa richness sample_tibble spreadplot summarize_phyloseq tax_tibble taxa time_normalize time_sort timesplit top top_taxa transform

Dependencies:ade4 ape bayesm Biobase BiocGenerics biomformat Biostrings cli cluster codetools compositions cpp11 crayon data.table DEoptimR digest dplyr farver foreach generics ggplot2 glue gtable igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv multtest nlme permute phyloseq pillar pixmap pkgconfig plyr purrr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang robustbase Rtsne S4Vectors S7 scales Seqinfo sp stringi stringr survival tensorA tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr XVector

Introduction to the microbiome R package

Introduction | Installation | Further reading | Acknowledgements

Rendered fromvignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
R package for microbiome studies	microbiome-package microbiome
Abundance Matrix from Phyloseq	ab, abundances otu
Adds 'best_hist' to a 'phyloseq-class' Object	add_besthit
Add 'refseq' Slot for 'dada2' based 'phyloseq' Object	add_refseq
Aggregate Rare Groups	aggregate_rare
Aggregate Taxa	aggregate_taxa
Global Ecosystem State Variables	alpha
Cross Correlation Wrapper	associate cross_correlate
HITChip Atlas with 1006 Western Adults	atlas1006
Pick Baseline Timepoint Samples	baseline
Bimodality Analysis	bimodality
Sarle's Bimodality Coefficient	bimodality_sarle
Abundance Boxplot	boxplot_abundance
Alpha Boxplot	boxplot_alpha
Convert Correlation Matrix into a Table	cmat2table
Collapse Replicate Samples	collapse_replicates
Core Microbiota	core filter_prevalent
Core Abundance	core_abundance
Core Heatmap	core_heatmap
Core Matrix	core_matrix
Core Taxa	core_members prevalent_taxa
Coverage Index	coverage
Default Colors	default_colors
Density Plot	densityplot
Diet Swap Data	dietswap
Divergence within a Sample Group	divergence
Diversity Index	diversity
Dominance Index	dominance
Dominant taxa	dominant
Evenness Index	evenness
Find Optima	find_optima
gktau	gktau
Age Classes	group_age
Body-Mass Index (BMI) Classes	group_bmi
Association Heatmap	heat
HITChip Taxonomy	hitchip.taxonomy
Univariate Bimodality Plot	hotplot
Gini Index	inequality
Intermediate Stability	intermediate_stability
Test Compositionality	is_compositional
Log-Modulo Skewness Rarity Index	log_modulo_skewness
Low Abundance Index	low_abundance
Map Taxonomic Levels	map_levels
Merge Taxa	merge_taxa2
Retrieve Phyloseq Metadata as Data Frame	meta
Multimodality Score	multimodality
Neatmap Sorting	neat
Neatmap Sorting	neatsort
Overlap Measure	overlap
Probiotics Intervention Data	peerj32
Visualize Samples of a Microbiota Atlas	plot_atlas
Taxonomic Composition Plot	plot_composition
Visualize OTU Core	plot_core
Plot Density	plot_density
Plot Frequencies	plot_frequencies
Landscape Plot	plot_landscape
Visually Weighted Regression Plot	plot_regression
Visualize Prevalence Distributions for Taxa	plot_taxa_prevalence
Variation Line Plot	plot_tipping
Bootstrapped Potential Analysis	potential_analysis
Potential Analysis for Univariate Data	potential_univariate
OTU Prevalence	prevalence
Convert 'phyloseq-class' object to long data format	psmelt2
Rare Microbiota	rare
Rare (Non-Core) Abundance Index	rare_abundance
Rare Taxa	rare_members
Rarity Index	rarity
Read BIOM File into a Phyloseq Object	read_biom2phyloseq
Read Simple OTU Tables into a Phyloseq Object	read_csv2phyloseq
Read Mothur Output into a Phyloseq Object	read_mothur2phyloseq
Import phyloseq Data	read_phyloseq
Total Read Count	readcount
Exclude Samples	remove_samples
Exclude Taxa	remove_taxa
Richness Index	richness
Abundance Spread Plot	spreadplot
Summarize phyloseq object	summarize_phyloseq
Taxa Names	taxa
Utilities For 'phyloseq-class' Slots to Tibbles	combine_otu_tax otu_tibble sample_tibble tax_tibble TibbleUtilites
Normalize Phyloseq Metadata Time Field	time_normalize
Temporal Sorting Within Subjects	time_sort
Time Split	timesplit
Identify Top Entries	top
Top Taxa	top_taxa
Data Transformations for phyloseq Objects	transform