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:
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)
NEWS
# Install 'jrSiCKLSNMF' in R: |
install.packages('jrSiCKLSNMF', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- SimData - A simulated dataset for use with jrSiCKLSNMF
- SimSickleJrSmall - A small SickleJr object containing a subset of data from the SimData data object. Contains the completed analysis from the 'Getting Started' vignette for a small subset of 10 cells with 150 genes and 700 peaks. The clusters derived from this dataset are not accurate; this dataset is intended for use with code examples.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:297d39d533. Checks:OK: 1 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 28 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 28 2024 |
Exports:AddSickleJrMetadataBuildKNNGraphLaplaciansBuildSNNGraphLaplaciansCalculateUMAPSickleJrClusterSickleJrCreateSickleJrDetermineClustersDetermineDFromIRLBAGenerateWmatricesandHmatrixjrSiCKLSNMFMinibatchDiagnosticPlotNormalizeCountMatricesPlotLossvsLatentFactorsPlotSickleJrUMAPRunjrSiCKLSNMFSetLambdasandRowRegSetWandHfromWHinitialsSickleJr
Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroombslibcachemcarcarDataclasscliclusterclValidcodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydendextendDerivdigestdoBydplyrdqrngDTedgeRellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtableherehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobanditeratorsjquerylibjsonlitekknnknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapodmgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbapplypbkrtestpillarpkgconfigplyrpngpolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRcppTOMLRdpackreshape2reticulaterlangrmarkdownrprojrootRSpectrarstatixrsvdS4ArraysS4VectorssassScaledMatrixscalesscatterplot3dscranscuttleSingleCellExperimentsitmosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsumaputf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc
Getting started with jrSiCKLSNMF
Rendered fromGetting_Started.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2023-07-06
Started: 2023-07-06
Getting started with jrSiCKLSNMF with an L2 Norm Constraint on the columns of H
Rendered fromGetting_Started_L2_Norm.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2023-07-06
Started: 2023-07-06
Mini-batch jrSiCKLSNMF Tutorial
Rendered fromMinibatch_jrSiCKLKSNMF.Rmd
usingknitr::rmarkdown
on Nov 28 2024.Last update: 2023-07-06
Started: 2023-07-06