Introduction | Batch effect correction on a single omic | About ARSyN | ARSyN method overview | How to cite ARSyN | Example: Yeast expression data | ARSyNbac input data | ARSyNbac correction | ARSyNbac batch effect correction | ARSyNbac noise reduction | ARSyNbac both modalities | Batch effect correction on a multiomic dataset | About MultiBaC | MultiBaC method overview | How to cite MultiBaC | Example: Yeast multiomic dataset | MultiBaC input data | MultiBaC correction | Running MultiBaC step by step | PLS model fitting | Prediction of missing omics | Batch effect correction | Visualization of ARSyN and MultiBaC results | Inner correlation in PLS models | Batch effect estimation plot | PCA plots | Session info | References
Package: MultiBaC 1.23.0
The package maintainer
MultiBaC: Multiomic Batch effect Correction
MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.
Authors:
MultiBaC_1.23.0.tar.gz
MultiBaC_1.23.0.zip(r-4.7)MultiBaC_1.23.0.zip(r-4.6)MultiBaC_1.23.0.zip(r-4.5)
MultiBaC_1.23.0.tgz(r-4.6-any)MultiBaC_1.23.0.tgz(r-4.5-any)
MultiBaC_1.23.0.tar.gz(r-4.7-any)MultiBaC_1.23.0.tar.gz(r-4.6-any)
MultiBaC_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MultiBaC/json (API)
| # Install 'MultiBaC' in R: |
| install.packages('MultiBaC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:MultiBaC-1.23.0(bioc 3.24)MultiBaC-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.
softwarestatisticalmethodprincipalcomponentdatarepresentationgeneexpressiontranscriptionbatcheffect
Last updated from:b8f3d4e7d4. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 183 | ||
| linux-devel-x86_64 | OK | 264 | ||
| source / vignettes | OK | 257 | ||
| linux-release-x86_64 | OK | 269 | ||
| macos-release-arm64 | OK | 150 | ||
| macos-oldrel-arm64 | OK | 120 | ||
| windows-devel | OK | 165 | ||
| windows-release | OK | 162 | ||
| windows-oldrel | OK | 167 | ||
| wasm-release | OK | 181 |
Exports:ARSyNbacbatchCorrectionbatchEstPlotcreateMbacexplained_varPlotgenMissingOmicsgenModelListinner_relPlotMultiBaCplot_pcaQ2_plotsummary.mbac
Dependencies:abindaskpassbase64encBiobaseBiocBaseUtilsBiocGenericsbslibcachemcalibrateclicpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomefsgenericsGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentMultiDataSetopensslotelpcaMethodspillarpkgconfigplotlyplotrixpromisespurrrqqmanR6rappdirsRColorBrewerRcpprlangrmarkdownroplsS4ArraysS4VectorsS7sassscalesSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Transcription rate data from yeast | A.gro |
| Gene expression data from yeast | A.rna |
| ARSyNbac | ARSyNbac |
| Gene translation rate data from yeast | B.ribo |
| Gene expression data from yeast | B.rna |
| batchCorrection | batchCorrection |
| batchEstPlot | batchEstPlot |
| Protein binded mRNA data from yeast | C.par |
| Gene expression data from yeast | C.rna |
| createMbac | createMbac |
| explained_varPlot | explained_varPlot |
| genMissingOmics | genMissingOmics |
| genModelList | genModelList |
| inner_relPLot | inner_relPlot |
| MultiBaC | MultiBaC-package MultiBaC |
| A distributed yeast multiomic dataset | multiyeast |
| plot_pca | plot_pca |
| Plot Method for mbac | plot,mbac-method plot.mbac |
| Q2_plot | Q2_plot |
| summary.mbac | summary.mbac |
