Package: nipalsMCIA 1.3.0

Maximilian Mattessich

nipalsMCIA: Multiple Co-Inertia Analysis via the NIPALS Method

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

Authors:Maximilian Mattessich [cre], Joaquin Reyna [aut], Edel Aron [aut], Anna Konstorum [aut]

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nipalsMCIA.pdf |nipalsMCIA.html✨
nipalsMCIA/json (API)
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Bug tracker:https://github.com/muunraker/nipalsmcia/issues

On BioConductor:nipalsMCIA-1.3.0(bioc 3.20)nipalsMCIA-1.2.0(bioc 3.19)

bioconductor-package

28 exports 1.45 score 92 dependencies

Last updated 2 months agofrom:3ebb28fe18

Exports:block_preprocblock_weights_heatmapcc_preproccol_preprocdeflate_block_bldeflate_block_gsextract_from_maeget_colorsget_metadata_colorsget_tvglobal_scores_eigenvalues_plotglobal_scores_heatmapgsea_reportnipals_iternipals_multiblocknmb_get_blnmb_get_bsnmb_get_bs_weightsnmb_get_eigsnmb_get_glnmb_get_gsnmb_get_metadataord_loadingspredict_gsprojection_plotsimple_maevis_load_ordvis_load_plot

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurldata.tableDelayedArraydigestdoParalleldplyrfansifarverfastmatchfgseaforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeMultiAssayExperimentmunsellnlmeopensslpillarpkgconfigpngpracmapurrrR6RColorBrewerRcppRcppEigenrjsonrlangRSpectraS4ArraysS4VectorsscalesshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc