Package: MBECS 1.11.0

Michael Olbrich

MBECS: Evaluation and correction of batch effects in microbiome data-sets

The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

Authors:Michael Olbrich [aut, cre]

MBECS_1.11.0.tar.gz
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MBECS.pdf |MBECS.html✨
MBECS/json (API)
NEWS

# Install 'MBECS' in R:
install.packages('MBECS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rmolbrich/mbecs/issues

Datasets:
  • dummy.list - Mock-up microbiome abundance table and meta-data.
  • dummy.mbec - Mock-up microbiome abundance table and meta-data.
  • dummy.ps - Mock-up microbiome abundance table and meta-data.

On BioConductor:MBECS-1.9.0(bioc 3.20)MBECS-1.8.0(bioc 3.19)

batcheffectmicrobiomereportwritingvisualizationnormalizationqualitycontrol

4.60 score 4 stars 4 scripts 278 downloads 38 exports 133 dependencies

Last updated 23 days agofrom:f5687580c8. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 31 2024

Exports:.mbecGetData.mbecGetPhyloseq.mbecSetDatacolinScorembecBoxmbecBoxPlotmbecCorrectionMbecDatambecDummymbecGetDatambecGetPhyloseqmbecHeatmbecHeatPlotmbecHelpFactormbecLMmbecMixedVariancembecModelVariancembecMosaicmbecMosaicPlotmbecPCAmbecPCAPlotmbecProcessInputmbecPVCAStatsPlotmbecRDAStatsPlotmbecReportPostmbecReportPrelimmbecRLEmbecRLEPlotmbecRunCorrectionsmbecSCOEFStatsPlotmbecSetDatambecTestModelmbecTransformmbecValidateModelmbecVarianceStatsmbecVarianceStatsPlotpercentileNormposcore

Dependencies:ade4annotateAnnotationDbiapeaskpassbase64encBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitbit64blobbootbslibcachemcliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestdplyredgeRevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegridExtragtablehighrhtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalme4lmerTestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamulttestmunsellnlmenloptrnumDerivopensslpermutepheatmapphyloseqpillarpixmappkgconfigplogrplyrpngpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownRSQLiteruvS4VectorssassscalessnowspstatmodstringistringrsurvivalsvasystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsveganviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

MBECS introduction

Rendered frommbecs_vignette.Rmdusingknitr::knitron Oct 30 2024.

Last update: 2022-02-22
Started: 2021-11-09

Readme and manuals

Help Manual

Help pageTopics
Mbec-Data Getter.mbecGetData
Return Phyloseq after correction.mbecGetPhyloseq
Mbec-Data Setter.mbecSetData
Variable Correlation Linear (Mixed) ModelscolinScore
Mock-up microbiome abundance table and meta-data.dummy.list
Mock-up microbiome abundance table and meta-data.dummy.mbec
Mock-up microbiome abundance table and meta-data.dummy.ps
Partial Least Squares Discriminant Analysis ComputationexternalPLSDA
Combat Batch Effects (ComBat)mbecBat
Batch Mean Centering (BMC)mbecBMC
Feature Differential Abundance Box-PlotmbecBox
Variability boxes plotting functionmbecBoxPlot
Centered Log-Ratio TransformationmbecCLR
Batch Effect Correction WrappermbecCorrection
Define MbecData-classMbecData
Calculate matrix residualsmbecDeflate
Creates a dummy data-set with abundance matrix and meta-data.mbecDummy
Calculate explained variance using CCAmbecExplainedVariance
Mbec-Data GettermbecGetData
Mbec-Data GettermbecGetData,MbecData-method
Return Phyloseq after correctionmbecGetPhyloseq
Return Phyloseq after correctionmbecGetPhyloseq,MbecData-method
Feature Differential Abundance HeatmapmbecHeat
Heatmap plotting functionmbecHeatPlot
Check If Covariates Are FactorsmbecHelpFactor
Linear (Mixed) Model Feature to Batch FitmbecLM
Mixed Model Variance-Component ExtractionmbecMixedVariance
Estimate Explained VariancembecModelVariance
Estimate Explained Variance with Linear ModelsmbecModelVarianceLM
Estimate Explained Variance with Linear Mixed ModelsmbecModelVarianceLMM
Estimate Explained Variance with Principal Variance Component AnalysismbecModelVariancePVCA
Estimate Explained Variance with Redundancy AnalysismbecModelVarianceRDA
Estimate Explained Variance with Silhouette CoefficientmbecModelVarianceSCOEF
Mosaic Sample Group AllocationmbecMosaic
Mosaic plotting functionmbecMosaicPlot
Principal Component Analysis PlotmbecPCA
Principal Component Analysis Plot for MbecDatambecPCA,MbecData-method
PCA plotting functionmbecPCAPlot
Partial Least Squares Discriminant AnalysismbecPLSDA
Percentile Normalization (PN)mbecPN
Mbec-Data Constructor WrappermbecProcessInput
Mbec-Data Constructor WrappermbecProcessInput,list-method
Mbec-Data Constructor WrappermbecProcessInput,MbecData-method
Mbec-Data Constructor WrappermbecProcessInput,phyloseq-method
Plot Proportion of Variance for PVCAmbecPVCAStatsPlot
Remove Batch Effects (RBE)mbecRBE
Plot Proportion of Variance for pRDAmbecRDAStatsPlot
Constructs a comparative report of batch corrected data.mbecReportPost
Constructs an initial report of a single data-set.mbecReportPrelim
Relative Log Expression PlotmbecRLE
RLE plotting functionmbecRLEPlot
Run Correction PipelinembecRunCorrections
Remove unwanted Variation 2 (RUV-2)mbecRUV2
Remove Unwanted Variation 3 (RUV-3)mbecRUV3
Remove Unwanted Variation 4 (RUV-4)mbecRUV4
MBECS: Evaluation and correction of batch effects in microbiome data-sets.MBECS
Plot Silhouette CoefficientmbecSCOEFStatsPlot
Mbec-Data SettermbecSetData
Mbec-Data SettermbecSetData,MbecData-method
Surrogate variable Analysis (SVA)mbecSVA
Singular Value Decomposition (SVD)mbecSVD
Check If Model Is EstimablembecTestModel
Normalizing TransformationsmbecTransform
Capitalize Word BeginningmbecUpperCase
Validate Linear (Mixed) ModelsmbecValidateModel
Wrapper for Model Variable Variance ExtractionmbecVarianceStats
Model Variable Variance Extraction from LMmbecVarianceStatsLM
Model Variable Variance Extraction from LMMmbecVarianceStatsLMM
Plot Proportion of Variance for L(M)MmbecVarianceStatsPlot
Percentile NormalizationpercentileNorm
Percentile of Scoreposcore