Package: phenomis 1.7.0
Etienne A. Thevenot
phenomis: Postprocessing and univariate analysis of omics data
The 'phenomis' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).
Authors:
phenomis_1.7.0.tar.gz
phenomis_1.7.0.zip(r-4.5)phenomis_1.7.0.zip(r-4.4)phenomis_1.7.0.zip(r-4.3)
phenomis_1.7.0.tgz(r-4.4-any)phenomis_1.7.0.tgz(r-4.3-any)
phenomis_1.7.0.tar.gz(r-4.5-noble)phenomis_1.7.0.tar.gz(r-4.4-noble)
phenomis_1.7.0.tgz(r-4.4-emscripten)phenomis_1.7.0.tgz(r-4.3-emscripten)
phenomis.pdf |phenomis.html✨
phenomis/json (API)
NEWS
| # Install 'phenomis' in R: |
| install.packages('phenomis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:phenomis-1.7.0(bioc 3.20)phenomis-1.6.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:d35e2b6ce7
Exports:annotatingannotating_parametersclusteringcorrectingfilteringgg_barplotgg_boxplotgg_piegg_volcanoplothypotestinginspectingnormalizingreadingreducingtransformingvennplotwriting
Dependencies:abindaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiodbbiodbChebibitbit64bitopsblobbriobslibBWStestcachemcalibratecallrchkclicolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydescdiffobjdigestdplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgit2rgluegmpgtablehighrhmshtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrkSampleslabelinglambda.rlaterlatticelazyevallgrlifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemultcompViewMultiAssayExperimentMultiDataSetmunsellmvtnormnlmeopensslpillarpkgbuildpkgconfigpkgloadplogrplotlyplyrPMCMRpluspraiseprettyunitsprocessxprogresspromisespspurrrqqmanR6rangerrappdirsRColorBrewerRcppRcppEigenRCurlrematch2rlangrmarkdownRmpfrroplsrprojrootRSQLiteS4ArraysS4VectorssassscalesSparseArraystatmodstringistringrSummarizedExperimentSuppDistssystestthattibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsVennDiagramviridisLitewaldowithrxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Postprocessing and univariate analysis of omics data | phenomis-package phenomis |
| MS annotation | annotating annotating,ExpressionSet-method annotating,MultiAssayExperiment-method annotating,MultiDataSet-method annotating,SummarizedExperiment-method annotating_parameters |
| clustering | clustering clustering,ExpressionSet-method clustering,MultiAssayExperiment-method clustering,MultiDataSet-method clustering,SummarizedExperiment-method |
| correcting | correcting correcting,ExpressionSet-method correcting,MultiAssayExperiment-method correcting,MultiDataSet-method correcting,SummarizedExperiment-method |
| Filtering of the features (and/or samples) with a high proportion of NAs or a low variance | filtering filtering,ExpressionSet-method filtering,MultiAssayExperiment-method filtering,MultiDataSet-method filtering,SummarizedExperiment-method |
| Barplot with ggplot2 | gg_barplot |
| Boxplot with ggplot2 | gg_boxplot |
| Pie with ggplot2 | gg_pie |
| Volcano plot with ggplot2 | gg_volcanoplot |
| Univariate hypothesis testing | hypotesting hypotesting,ExpressionSet-method hypotesting,MultiAssayExperiment-method hypotesting,MultiDataSet-method hypotesting,SummarizedExperiment-method |
| Inspecting | inspecting inspecting,ExpressionSet-method inspecting,MultiAssayExperiment-method inspecting,MultiDataSet-method inspecting,SummarizedExperiment-method |
| Normalization of the data matrix intensities | normalizing normalizing,ExpressionSet-method normalizing,MultiAssayExperiment-method normalizing,MultiDataSet-method normalizing,SummarizedExperiment-method |
| reading | reading |
| Grouping chemically redundant MS1 features | reducing reducing,ExpressionSet-method reducing,MultiAssayExperiment-method reducing,MultiDataSet-method reducing,SummarizedExperiment-method |
| Transformation of the data matrix intensities | transforming transforming,ExpressionSet-method transforming,MultiAssayExperiment-method transforming,MultiDataSet-method transforming,SummarizedExperiment-method |
| Venn diagram with VennDiagram | vennplot |
| Exporting a SummarizedExperiment (or MultiAssayExperiment) instance into (subfolders with) the 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', 'variableMetadata.tsv' | writing writing,ExpressionSet-method writing,MultiAssayExperiment-method writing,MultiDataSet-method writing,SummarizedExperiment-method |
