Package: PathoStat 1.31.0
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_1.31.0.tar.gz
PathoStat_1.31.0.zip(r-4.5)PathoStat_1.31.0.zip(r-4.4)PathoStat_1.31.0.zip(r-4.3)
PathoStat_1.31.0.tgz(r-4.4-any)PathoStat_1.31.0.tgz(r-4.3-any)
PathoStat_1.31.0.tar.gz(r-4.5-noble)PathoStat_1.31.0.tar.gz(r-4.4-noble)
PathoStat_1.31.0.tgz(r-4.4-emscripten)PathoStat_1.31.0.tgz(r-4.3-emscripten)
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/issues
On BioConductor:PathoStat-1.31.0(bioc 3.20)PathoStat-1.30.0(bioc 3.19)
Last updated 2 months agofrom:abc2a55064
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.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgbuildpkgconfigpkgdownpkgloadplotlyplyrpngpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRcppEigenrematch2remotesrentrezreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownROCRroxygen2rprojrootrstudioapirversionsS4ArraysS4VectorssassscalessessioninfoshapeshinyshinyjssnowsourcetoolsspSparseArraystatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytexUCSC.utilsurlcheckerusethisutf8vctrsveganviridisLitewaldowebshotwhiskerwithrxfunXMLxml2xopenxtableXVectoryamlzipzlibbioc