Package: microbiomeExplorer 1.23.0

Janina Reeder

microbiomeExplorer: Microbiome Exploration App

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

Authors:Joseph Paulson [aut], Janina Reeder [aut, cre], Mo Huang [aut], Genentech [cph, fnd]

microbiomeExplorer_1.23.0.tar.gz
microbiomeExplorer_1.23.0.zip(r-4.7)microbiomeExplorer_1.23.0.zip(r-4.6)microbiomeExplorer_1.23.0.zip(r-4.5)
microbiomeExplorer_1.23.0.tgz(r-4.6-any)microbiomeExplorer_1.23.0.tgz(r-4.5-any)
microbiomeExplorer_1.23.0.tar.gz(r-4.7-any)microbiomeExplorer_1.23.0.tar.gz(r-4.6-any)
microbiomeExplorer_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
microbiomeExplorer/json (API)

# Install 'microbiomeExplorer' in R:

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

On BioConductor:microbiomeExplorer-1.23.0(bioc 3.24)microbiomeExplorer-1.22.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

classification clustering geneticvariability differentialexpression microbiome metagenomics normalization visualization multiplecomparison sequencing software immunooncology

4.04 score 11 scripts 37 exports 183 dependencies

Last updated from:2398fa4486. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	202
linux-devel-x86_64	NOTE	305
source / vignettes	OK	280
linux-release-x86_64	NOTE	265
macos-release-arm64	NOTE	132
macos-oldrel-arm64	NOTE	148
windows-devel	NOTE	181
windows-release	NOTE	226
windows-oldrel	NOTE	172
wasm-release	OK	208

Exports:addFeatData addPhenoData aggFeatures aggregationTabUI calculatePCAs computeDistMat corrAnalysisUI corrFeature corrPhenotype dataInputUI diffAnalysisUI extendPhenoData featureAnalysisUI featureTableUI filterByPheno filterMEData interAnalysisUI intraAnalysisUI longAnalysisUI makeQCPlot normalizeData phenotypeTableUI plotAbundance plotAlpha plotAvgAbundance plotBeta plotHeatmap plotLongFeature plotlyHistogram plotlySampleBarplot plotSingleFeature readData replaceWithUnknown reportListUI rollDownFeatures runDiffTest runMicrobiomeExplorer

Dependencies:abind askpass assertthat backports base64enc BH Biobase BiocGenerics BiocParallel biomformat bit bit64 bitops boot broom bslib ca cachem callr car carData caTools cli clipr cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DelayedArray dendextend Deriv DESeq2 digest doBy dplyr DT egg evaluate farver fastmap fontawesome forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options gclus generics GenomicRanges ggplot2 glmnet glue gplots gridExtra gtable gtools heatmaply highr hms htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 lmtest locfit lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise metagenomeSeq mgcv mime minqa modelr nlme nloptr nnet numDeriv openssl otel pbkrtest permute pillar pkgconfig plotly plyr prettyunits processx progress promises ps purrr qap quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas registry reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo seriation shape shiny shinycssloaders shinydashboard shinyjs shinyWidgets snow sourcetools SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tinytex TSP tzdb urca utf8 vctrs vegan viridis viridisLite vroom webshot withr Wrench xfun xtable XVector yaml zoo

Using Microbiome Explorer application to analyze amplicon sequencing data

Rendered fromexploreMouseData.Rmdusingknitr::rmarkdown

Last update: 2020-10-06
Started: 2020-07-27

Help page	Topics
Abundance Heatmap module - server	abundanceHeatmap
Abundance Heatmap module - UI	abundanceHeatmapUI
Adds a config call based on plotly::config	add_plotly_config
Adds a layout call based on plotly::layout	add_plotly_layout
Add feature data to MRobj.	addFeatData
Add phenotype data to object.	addPhenoData
Aggregates counts by level	aggFeatures
Aggregation module server function	aggregationTab
Aggregation module ui function	aggregationTabUI
Alpha Diversity module - server	alphaDiversity
Alpha Diversity module - UI	alphaDiversityUI
Relative abundance plot module - server	avgAbundance
Relative abundance plot module - UI	avgAbundanceUI
Beta Diversity module - server	betaDiversity
Beta Diversity module - UI	betaDiversityUI
Server side for the analysis input module handling analysis control	betaInput
Main beta analysis input module. Set up to handle all analysis tabs in the app depending on given parameters	betaInputUI
Creates an empty plotly plot using the given labels on the x and y axis	buildEmptyPlotlyPlot
Sets up a dataframe used by several plotting functions by joining the required data with relevant phenotype data	buildPlottingDF
Function to compute the PCAs for a given distance matrix	calculatePCAs
Helper function to calculate the confidence interval for a cor.test	computeCI_Interval
Function to compute the distance matrix using vegdist from the vegan package	computeDistMat
corr Analysis Module - server	corrAnalysis
corr Analysis Module - UI	corrAnalysisUI
Scatterplot of two features	corrFeature
Server side for the analysis input module handling analysis control	corrInput
Main correlation analysis input module. Handles correlation analysis tab in the app	corrInputUI
Scatterplot of a feature and a phenotype	corrPhenotype
Makes header for R script	createHeader
Main Data input server where the user selects files to upload to the app or connects to database	dataInput
Main Data input UI where the user selects files to upload to the app or connects to database	dataInputUI
Produce design matrix of pairwise comparisons	designPairs
diff Analysis Module - server	diffAnalysis
Diff Analysis Module - UI	diffAnalysisUI
Server side for the analysis input module handling analysis control	diffInput
Main diffanalysis input module. Set up to handle diff analysis tabs in the app depending on given parameters	diffInputUI
Differential analysis module server code	diffTable
Differential Analysis module UI	diffTableUI
Extends existing phenodata for an object	extendPhenoData
Feature plot module - server	featAbundance
Feature plot module - UI	featAbundanceUI
feature Analysis Module - server	featureAnalysis
feature Analysis Module - UI	featureAnalysisUI
Feature correlation analysis server module	featureCorr
Feature correlation analysis module UI	featureCorrUI
Server side for the feature analysis input module	featureInput
Main feature analysis input module. Set up to handle all analysis tabs in the app depending on given parameters	featureInputUI
Feature table module server code	featureTable
Feature table UI module	featureTableUI
Module handling file upload for the application: server	fileUpload
Module handling file upload for the application: UI In a deployed version this module should be replaced with database access	fileUploadUI
Function to filter the MRexperiment by certain phenotype values	filterByPheno
Function to filter the MRexperiment data by numerical parameters	filterMEData
Generates report	generateReport
Helper function returning the fData modifications as strings for report generation	getFeatModCode
Helper function returning the fData modifications as strings for report generation	getFeatSplitCode
Helper function assigning different file extensions to specific short texts identifying the types	getFileType
Helper function to filter phenodata for interesting phenotypes to be used for filtering or subsetting	getFilterChoices
Function to find a non-empty facet in the last row. This will be the one to be connected to the plot legend to avoid duplicates within	getLegendLevel
Helper function returning the code used to modify the data types of the pheno table	getPhenoChanges
Helper function returning the code used to modify the phenotable as a string	getPhenoModCode
Helper function to account for issues plotly has with very small widths (these end up being 1 and cover the entire plotting area)	getWidths
Server side for the analysis input module handling analysis control	heatmapInput
Heatmap analysis input module. Set up to handle all analysis tabs in the app depending on given parameters	heatmapInputUI
inter Analysis Module - server	interAnalysis
inter Analysis Module - UI	interAnalysisUI
Intra Analysis Module - server	intraAnalysis
Intra Analysis Module - UI	intraAnalysisUI
Server side for the intra analysis input module	intraInput
Main intra analysis input module. Set up to handle all analysis tabs in the app depending on given parameters	intraInputUI
long Analysis Module - server	longAnalysis
Long Analysis Module - UI	longAnalysisUI
Server side for the analysis input module handling analysis control	longInput
Main diffanalysis input module. Set up to handle diff analysis tabs in the app depending on given parameters	longInputUI
Longitudinal analysis module server code	longResults
Longitudinal Analysis module UI	longResultsUI
Plots sequencing statistics scatterplot	makeQCPlot
Calls appropriate normalization functions depending on input parameter The two available methods included in the package are based on either calculating proportions or by using cumulative sum scaling (CSS), Paulson, et al. Nat Meth 2013.	normalizeData
Helper function used to build a correct interactionName based on the chosen columns	parseInteractionName
Phenotype correlation analysis server module	phenotypeCorr
Phenotype correlation analysis module	phenotypeCorrUI
Phenotype table server module	phenotypeTable
Phenotype table UI module	phenotypeTableUI
Plot relative abundance	plotAbundance
Plot alpha diversity	plotAlpha
Plot average relative abundance	plotAvgAbundance
Plot beta diversity	plotBeta
Plot heatmap	plotHeatmap
Plot longitudinal features	plotLongFeature
Function plotting a plotly histogram on the given histvalue	plotlyHistogram
Function plotting a barplot showing number of OTUs per samples	plotlySampleBarplot
Plot features	plotSingleFeature
Reads in data	readData
Relative abundance plot module - server	relAbundance
Relative abundance plot module - UI	relAbundanceUI
Helper function to replace any un-annotated features with the term unknown	replaceWithUnknown
Report tab module server	reportList
report tab ui	reportListUI
Report Row	reportRow
Report row module consisting of a checkbox, image and description/R code area	reportRowUI
Helper function which rolls down annotated from closest higher order with annotation	rollDownFeatures
Performs differential abundance testing	runDiffTest
Main function to start the Microbiome Explorer Shiny app via a command line call	runMicrobiomeExplorer

Package: microbiomeExplorer 1.23.0

microbiomeExplorer: Microbiome Exploration App

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