Package: animalcules 1.29.0

W. Evan Johnson

animalcules: Interactive microbiome analysis toolkit

animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

Authors:W. Evan Johnson [aut, cre], Yue Zhao [aut], Anthony Federico [aut], Jessica Anderson [ctr]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
animalcules/json (API)

# Install 'animalcules' in R:

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

Bug tracker:https://github.com/wejlab/animalcules/issues

On BioConductor:animalcules-1.29.0(bioc 3.24)animalcules-1.28.0(bioc 3.23)

microbiome metagenomics coverage visualization

7.12 score 56 stars 34 scripts 1 mentions 43 exports 179 dependencies

Last updated from:cecf678417. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	232
linux-devel-x86_64	OK	405
source / vignettes	OK	322
linux-release-x86_64	OK	450
macos-release-arm64	OK	200
macos-oldrel-arm64	OK	218
windows-devel	OK	287
windows-release	OK	299
windows-oldrel	OK	300
wasm-release	OK	221

Exports:alpha_div_boxplot alpha_div_test counts_to_logcpm counts_to_relabu df_char_to_factor differential_abundance dimred_pca dimred_pcoa dimred_tsne dimred_umap diversities diversities_help diversity_beta_boxplot diversity_beta_heatmap diversity_beta_NMDS diversity_beta_test do_alpha_div_test filter_categorize filter_summary_bar_density filter_summary_pie_box find_biomarker find_taxon_mat find_taxonomy find_taxonomy_300 gini_simpson grep_tid inverse_simpson is_categorical is_integer0 is_integer1 mae_pick_organisms mae_pick_samples pct2str percent read_pathoscope_data relabu_barplot relabu_boxplot relabu_heatmap run_animalcules shannon simpson_index upsample_counts write_to_biom

Dependencies:abind ape askpass assertthat base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bslib cachem caret class cli clock clue cluster codetools commonmark covr cpp11 crosstalk curl data.table DelayedArray DESeq2 diagram digest dirmult dplyr DT e1071 evaluate farver fastmap fBasics fontawesome forcats foreach formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggforce ggplot2 ggrepel globals glue gower gss gtable GUniFrac hardhat here highr htmltools htmlwidgets httpuv httr inline ipred IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lava lazyeval lifecycle limma listenv locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime modeest ModelMetrics MultiAssayExperiment nlme nnet numDeriv openssl otel parallelly permute pillar pkgconfig plotly plyr png polyclip pROC prodlim progressr promises proxy purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML recipes rentrez reshape2 reticulate rex rlang rmarkdown rmutil ROCit rpart rprojroot RSpectra S4Arrays S4Vectors S7 sass scales Seqinfo shape shiny shinyjs snow sourcetools SparseArray sparsevctrs spatial SQUAREM stable stabledist statip statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidyr tidyselect timechange timeDate timeSeries tinytex tsne tweenr tzdb umap utf8 vctrs vegan viridisLite withr xfun XML xtable XVector yaml

animalcules

Rendered fromanimalcules.Rmdusingknitr::rmarkdown

Last update: 2024-01-19
Started: 2018-11-27

Help page	Topics
Alpha diversity boxplot	alpha_div_boxplot
Get alpha diversity	alpha_div_test
Covert a counts table to a relative abundances table	counts_to_logcpm
Covert a counts table to a relative abundances table	counts_to_relabu
Factorize all categorical columns	df_char_to_factor
Differential abundance analysis	differential_abundance
Dimensionality reduction through PCA	dimred_pca
Dimensionality reduction through PCoA	dimred_pcoa
Dimensionality reduction through t-SNE	dimred_tsne
Dimensionality reduction through PCA	dimred_umap
Get alpha diversity	diversities
Get alpha diversity	diversities_help
Beta diversity boxplot	diversity_beta_boxplot
Beta diversity heatmap	diversity_beta_heatmap
Beta diversity NMDS plot	diversity_beta_NMDS
Perform a beta diversity test	diversity_beta_test
Alpha diversity statistical test	do_alpha_div_test
Categorize continuous variables	filter_categorize
Data visualization by bar plot / density plot	filter_summary_bar_density
Data visualization by pie chart / box plot	filter_summary_pie_box
Identify biomarkers	find_biomarker
Find the Taxonomy Information Matrix	find_taxon_mat
Find the taxonomy for unlimited tids	find_taxonomy
Find the taxonomy for maximum 300 tids	find_taxonomy_300
Get alpha diversity using gini	gini_simpson
Greps the tid from the given identifier string	grep_tid
Get alpha diversity using inverse simpson	inverse_simpson
Check if object is categorical	is_categorical
check if integer(0)	is_integer0
check if integer(1)	is_integer1
Modify organisms of multi-assay experiment object	mae_pick_organisms
Modify samples of multi-assay experiment object	mae_pick_samples
Converts decimal percentage to string with specified digits	pct2str
Format decimals to percentages	percent
Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data	read_pathoscope_data
Plot bar plots of sample and group level relative abundance	relabu_barplot
Plot boxplots comparing different organism prevalence across conditions	relabu_boxplot
Plot heatmap of sample level counts in logcpm	relabu_heatmap
Run animalcules shiny app	run_animalcules
Get alpha diversity using shannon	shannon
Get alpha diversity using simpson	simpson_index
Upsample a counts table to a higher taxon level	upsample_counts
Output biom	write_to_biom

Package: animalcules 1.29.0

animalcules: Interactive microbiome analysis toolkit

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