Package: jrSiCKLSNMF 1.2.1

Dorothy Ellis

jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.

Authors:Dorothy Ellis [aut, cre], Susmita Datta [ths], Kenneth Perkins [ctb], Renaud Gaujoux [ctb]

jrSiCKLSNMF_1.2.1.tar.gz
jrSiCKLSNMF_1.2.1.tar.gz(r-4.5-noble)jrSiCKLSNMF_1.2.1.tar.gz(r-4.4-noble)
jrSiCKLSNMF_1.2.1.tgz(r-4.4-emscripten)jrSiCKLSNMF_1.2.1.tgz(r-4.3-emscripten)
jrSiCKLSNMF.pdf |jrSiCKLSNMF.html✨
jrSiCKLSNMF/json (API)
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18 exports 0.00 score 177 dependencies 6 scripts 225 downloads

Last updated 1 years agofrom:297d39d533. Checks:OK: 1 NOTE: 1. Indexed: yes.

Exports:AddSickleJrMetadataBuildKNNGraphLaplaciansBuildSNNGraphLaplaciansCalculateUMAPSickleJrClusterSickleJrCreateSickleJrDetermineClustersDetermineDFromIRLBAGenerateWmatricesandHmatrixjrSiCKLSNMFMinibatchDiagnosticPlotNormalizeCountMatricesPlotLossvsLatentFactorsPlotSickleJrUMAPRunjrSiCKLSNMFSetLambdasandRowRegSetWandHfromWHinitialsSickleJr

Dependencies:abindaskpassbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroombslibcachemcarcarDataclasscliclusterclValidcodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydendextendDerivdigestdoBydplyrdqrngDTedgeRellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtableherehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobanditeratorsjquerylibjsonlitekknnknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapodmgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbapplypbkrtestpillarpkgconfigplyrpngpolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLRdpackreshape2reticulaterlangrmarkdownrprojrootRSpectrarstatixrsvdS4ArraysS4VectorssassScaledMatrixscalesscatterplot3dscranscuttleSingleCellExperimentsitmosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsumaputf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc