Package: animalcules 1.23.0

Jessica McClintock

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:Jessica McClintock [cre], Yue Zhao [aut], Anthony Federico [aut], W. Evan Johnson [aut]

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animalcules.pdf |animalcules.html✨
animalcules/json (API)

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

Peer review:

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

On BioConductor:animalcules-1.21.0(bioc 3.20)animalcules-1.20.0(bioc 3.19)

microbiomemetagenomicscoveragevisualization

7.51 score 52 stars 22 scripts 546 downloads 43 exports 183 dependencies

Last updated 18 days agofrom:1f256fc513. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:alpha_div_boxplotalpha_div_testcounts_to_logcpmcounts_to_relabudf_char_to_factordifferential_abundancedimred_pcadimred_pcoadimred_tsnedimred_umapdiversitiesdiversities_helpdiversity_beta_boxplotdiversity_beta_heatmapdiversity_beta_NMDSdiversity_beta_testdo_alpha_div_testfilter_categorizefilter_summary_bar_densityfilter_summary_pie_boxfind_biomarkerfind_taxon_matfind_taxonomyfind_taxonomy_300gini_simpsongrep_tidinverse_simpsonis_categoricalis_integer0is_integer1mae_pick_organismsmae_pick_samplespct2strpercentread_pathoscope_datarelabu_barplotrelabu_boxplotrelabu_heatmaprun_animalculesshannonsimpson_indexupsample_countswrite_to_biom

Dependencies:abindapeaskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcaretclasscliclockclueclustercodetoolscolorspacecommonmarkcovrcpp11crayoncrosstalkcurldata.tableDelayedArrayDESeq2diagramdigestdirmultdplyrDTe1071evaluatefansifarverfastmapfBasicsfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2ggrepelglobalsgluegowergssgtableGUniFrachardhatherehighrhtmltoolshtmlwidgetshttpuvhttrinlineipredIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelavalazyevallifecyclelimmalistenvlocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemodeestModelMetricsMultiAssayExperimentmunsellnlmennetnumDerivopensslparallellypermutepillarpkgconfigplotlyplyrpngpolyclippROCprodlimprogressrpromisesproxypurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLrecipesrentrezreshape2reticulaterexrlangrmarkdownrmutilROCitrpartrprojrootRSpectraS4ArraysS4VectorssassscalesshapeshinyshinyjssnowsourcetoolsSparseArrayspatialSQUAREMstablestablediststatipstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidyrtidyselecttimechangetimeDatetimeSeriestinytextsnetweenrtzdbUCSC.utilsumaputf8vctrsveganviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

animalcules

Yue Zhao, Anthony Federico, Evan Johnson

Rendered fromanimalcules.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Alpha diversity boxplotalpha_div_boxplot
Get alpha diversityalpha_div_test
Covert a counts table to a relative abundances tablecounts_to_logcpm
Covert a counts table to a relative abundances tablecounts_to_relabu
Factorize all categorical columnsdf_char_to_factor
Differential abundance analysisdifferential_abundance
Dimensionality reduction through PCAdimred_pca
Dimensionality reduction through PCoAdimred_pcoa
Dimensionality reduction through t-SNEdimred_tsne
Dimensionality reduction through PCAdimred_umap
Get alpha diversitydiversities
Get alpha diversitydiversities_help
Beta diversity boxplotdiversity_beta_boxplot
Beta diversity heatmapdiversity_beta_heatmap
Beta diversity NMDS plotdiversity_beta_NMDS
Perform a beta diversity testdiversity_beta_test
Alpha diversity statistical testdo_alpha_div_test
Categorize continuous variablesfilter_categorize
Data visualization by bar plot / density plotfilter_summary_bar_density
Data visualization by pie chart / box plotfilter_summary_pie_box
Identify biomarkersfind_biomarker
Find the Taxonomy Information Matrixfind_taxon_mat
Find the taxonomy for unlimited tidsfind_taxonomy
Find the taxonomy for maximum 300 tidsfind_taxonomy_300
Get alpha diversity using ginigini_simpson
Greps the tid from the given identifier stringgrep_tid
Get alpha diversity using inverse simpsoninverse_simpson
Check if object is categoricalis_categorical
check if integer(0)is_integer0
check if integer(1)is_integer1
Modify organisms of multi-assay experiment objectmae_pick_organisms
Modify samples of multi-assay experiment objectmae_pick_samples
Converts decimal percentage to string with specified digitspct2str
Format decimals to percentagespercent
Reads the data from PathoScope reports and returns a list of final guess relative abundance and count dataread_pathoscope_data
Plot bar plots of sample and group level relative abundancerelabu_barplot
Plot boxplots comparing different organism prevalence across conditionsrelabu_boxplot
Plot heatmap of sample level counts in logcpmrelabu_heatmap
Run animalcules shiny apprun_animalcules
Get alpha diversity using shannonshannon
Get alpha diversity using simpsonsimpson_index
Upsample a counts table to a higher taxon levelupsample_counts
Output biomwrite_to_biom