Package: PathoStat 1.33.0
Solaiappan Manimaran
PathoStat: PathoStat Statistical Microbiome Analysis Package
The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
Authors:
PathoStat_1.33.0.tar.gz
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PathoStat.pdf |PathoStat.html✨
PathoStat/json (API)
NEWS
| # Install 'PathoStat' in R: |
| install.packages('PathoStat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mani2012/pathostat/issues9 issues
On BioConductor:PathoStat-1.33.0(bioc 3.21)PathoStat-1.32.0(bioc 3.20)
microbiomemetagenomicsgraphandnetworkmicroarraypatternlogicprincipalcomponentsequencingsoftwarevisualizationrnaseqimmunooncology
Last updated 5 months agofrom:1f65914ec5. Checks:1 OK, 8 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 29 2025 |
| R-4.5-win | NOTE | Mar 29 2025 |
| R-4.5-mac | NOTE | Mar 29 2025 |
| R-4.5-linux | NOTE | Mar 29 2025 |
| R-4.4-win | NOTE | Mar 29 2025 |
| R-4.4-mac | NOTE | Mar 29 2025 |
| R-4.4-linux | NOTE | Mar 29 2025 |
| R-4.3-win | NOTE | Mar 29 2025 |
| R-4.3-mac | NOTE | Mar 29 2025 |
Exports:Bootstrap_LOOCV_LR_AUCChisq_Test_PamfindRAfromCountfindTaxonMatfindTaxonomyfindTaxonomy300Fisher_Test_PamGET_PAMgetShinyInputgetShinyInputCombatgetShinyInputOriggetSignatureFromMultipleGlmnetgrepTidloadPathoscopeReportsloadPstatlog2CPMLOOAUC_simple_multiple_noplot_one_dfLOOAUC_simple_multiple_one_dfpathostat1percentphyloseq_to_edgeRplotPCAPlotlyplotPCoAPlotlyreadPathoscopeDatarunPathoStatsavePstatsetShinyInputsetShinyInputCombatsetShinyInputOrigsummarizeTableTranslateIdToTaxLevelWilcox_Test_df
Dependencies:abindade4apeaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStylebiomformatBiostringsbitopsbookdownbrewbriobslibcachemcallrcaToolscirclizeclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorpcorcpp11crayoncredentialscrosstalkcurldata.tableDelayedArraydescDESeq2devtoolsdiffobjdigestdoParalleldownlitdplyrDTedgeRellipsisevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgdatagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgertGetoptLongggplot2ghgitcredsglmnetGlobalOptionsgluegmodelsgplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphiniIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgbuildpkgconfigpkgdownpkgloadplotlyplyrpngpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRcppEigenremotesrentrezreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownROCRroxygen2rprojrootrstudioapirversionsS4ArraysS4VectorssassscalessessioninfoshapeshinyshinyjssnowsourcetoolsspSparseArraystatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytexUCSC.utilsurlcheckerusethisutf8vctrsveganviridisLitewaldowebshotwhiskerwithrxfunXMLxml2xopenxtableXVectoryamlzip
Citation
To cite package ‘PathoStat’ in publications use:
Manimaran S, Bendall M, Diaz SV, Castro E, Faits T, Zhao Y, Federico AN, Johnson WE (2020). PathoStat: PathoStat Statistical Microbiome Analysis Package. R package version 1.33.0, https://bioconductor.org/packages/PathoStat.
ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.
Corresponding BibTeX entry:
@Manual{,
title = {PathoStat: PathoStat Statistical Microbiome Analysis
Package},
author = {Solaiappan Manimaran and Matthew Bendall and Sandro
Valenzuela Diaz and Eduardo Castro and Tyler Faits and Yue Zhao
and Anthony Nicholas Federico and W. Evan Johnson},
year = {2020},
note = {R package version 1.33.0},
url = {https://bioconductor.org/packages/PathoStat},
}
Readme and manuals
PathoStat: Statistical Microbiome Analysis Toolkit
PathoStat is a R shiny package, designed for performing Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files.
The package includes:
1. Data Summary and Filtering
2. Relative Abundance plots (Stacked Bar Plot, Heatmap)
3. Multiple species boxplot visualization
4. Diversity analysis (Alpha and Beta diversity)
5. Differential Expression (DEseq2, edgeR)
6. Dimension Reduction (PCA, PCoA)
7. Biomarker identification
runPathoStat is the pipeline function that generates the PathoStat report
and launches shiny app when in interactive mode. It combines all the functions
into one step.
Run Pathostat
To launch PathoStat in R, just enter the command:
runPathoStat()
Installation
To begin, install Bioconductor and simply run the following to automatically install PathoStat and all the dependencies as follows.
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("PathoStat")
If you want to install the latest development version of PathoStat from Github, use devtools to install it as follows:
require(devtools)
install_github("compbiomed/PathoStat")
If all went well you should now be able to load PathoStat:
require(PathoStat)
vignette('PathoStat-vignette', package='PathoStat')
runPathoStat()
