Package: biosigner 1.33.0
Etienne A. Thevenot
biosigner: Signature discovery from omics data
Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.
Authors:
biosigner_1.33.0.tar.gz
biosigner_1.33.0.zip(r-4.5)biosigner_1.33.0.zip(r-4.4)biosigner_1.33.0.zip(r-4.3)
biosigner_1.33.0.tgz(r-4.4-any)biosigner_1.33.0.tgz(r-4.3-any)
biosigner_1.33.0.tar.gz(r-4.5-noble)biosigner_1.33.0.tar.gz(r-4.4-noble)
biosigner_1.33.0.tgz(r-4.4-emscripten)biosigner_1.33.0.tgz(r-4.3-emscripten)
biosigner.pdf |biosigner.html✨
biosigner/json (API)
NEWS
| # Install 'biosigner' in R: |
| install.packages('biosigner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- diaplasma - Analysis of plasma from diabetic patients by LC-HRMS
On BioConductor:biosigner-1.33.0(bioc 3.20)biosigner-1.32.0(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:59069cf216
Exports:biosigngetAccuracyMNgetBiosigngetEsetgetMsetgetSignatureLsplotpredictshow
Dependencies:abindaskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcalibrateclassclicolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyre1071evaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentMultiDataSetmunsellnlmeopensslpillarpkgconfigplotlypromisesproxypurrrqqmanR6randomForestrappdirsRColorBrewerRcpprlangrmarkdownroplsS4ArraysS4VectorssassscalesSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Molecular signature discovery from omics data | biosigner-package biosigner |
| Builds the molecular signature. | biosign biosign,data.frame-method biosign,ExpressionSet-method biosign,matrix-method biosign,MultiAssayExperiment-method biosign,MultiDataSet-method biosign,MultiDataSet_method biosign,SummarizedExperiment-method |
| Class "biosign" | biosign-class |
| Class "biosignMultiDataSet" | biosignMultiDataSet-class |
| Analysis of plasma from diabetic patients by LC-HRMS | diaplasma |
| Accuracies of the full model and the models restricted to the signatures | getAccuracyMN getAccuracyMN,biosign-method |
| Getting the biosigner signature from the SummarizedExperiment object | getBiosign getBiosign,MultiAssayExperiment-method getBiosign,SummarizedExperiment-method |
| getEset method | biosign-method getEset getEset, getEset,biosign-method |
| getMset method | biosignMultiDataSet-method getMset getMset, getMset,biosignMultiDataSet-method |
| Signatures selected by the models | getSignatureLs getSignatureLs,biosign-method |
| Plot method for 'biosign' signature objects | plot,biosign,ANY-method plot,biosign-method plot,biosignMultiDataSet,ANY-method plot,biosignMultiDataSet-method plot.biosign plot.biosignMultiDataSet |
| Predict method for 'biosign' signature objects | predict,biosign-method predict.biosign |
| Show method for 'biosign' signature objects | show,biosign-method show.biosign |
