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)
NEWS

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • 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.

openblascppopenmp

3.18 score 6 scripts 228 downloads 18 exports 178 dependencies

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

TargetResultDate
Doc / VignettesOKNov 28 2024
R-4.5-linux-x86_64NOTENov 28 2024

Exports:AddSickleJrMetadataBuildKNNGraphLaplaciansBuildSNNGraphLaplaciansCalculateUMAPSickleJrClusterSickleJrCreateSickleJrDetermineClustersDetermineDFromIRLBAGenerateWmatricesandHmatrixjrSiCKLSNMFMinibatchDiagnosticPlotNormalizeCountMatricesPlotLossvsLatentFactorsPlotSickleJrUMAPRunjrSiCKLSNMFSetLambdasandRowRegSetWandHfromWHinitialsSickleJr

Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbootbroombslibcachemcarcarDataclasscliclusterclValidcodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydendextendDerivdigestdoBydplyrdqrngDTedgeRellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtableherehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesirlbaisobanditeratorsjquerylibjsonlitekknnknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapodmgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbapplypbkrtestpillarpkgconfigplyrpngpolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRcppTOMLRdpackreshape2reticulaterlangrmarkdownrprojrootRSpectrarstatixrsvdS4ArraysS4VectorssassScaledMatrixscalesscatterplot3dscranscuttleSingleCellExperimentsitmosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsumaputf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc

Getting started with jrSiCKLSNMF

Rendered fromGetting_Started.Rmdusingknitr::rmarkdownon 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.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2023-07-06
Started: 2023-07-06

Mini-batch jrSiCKLSNMF Tutorial

Rendered fromMinibatch_jrSiCKLKSNMF.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2023-07-06
Started: 2023-07-06

Readme and manuals

Help Manual

Help pageTopics
Add metadata to an object of class SickleJrAddSickleJrMetadata
Build KNN graphs and generate their graph LaplaciansBuildKNNGraphLaplacians
Build SNN graphs and generate their graph LaplaciansBuildSNNGraphLaplacians
Calculate the UMAP for an object of class SickleJrCalculateUMAPSickleJr
Cluster the \mathbf{H} matrixClusterSickleJr
Create an object of class SickleJrCreateSickleJr
Perform clustering diagnosticsDetermineClusters
Create elbow plots of the singular values derived from IRLBA to determine D for large datasetsDetermineDFromIRLBA
Initialize the \mathbf{W} matrices in each modality and the shared \mathbf{H} matrixGenerateWmatricesandHmatrix
Run jrSiCKLSNMF outside of a SickleJr objectjrSiCKLSNMF
Plot a diagnostic plot for the mini-batch algorithmMinibatchDiagnosticPlot
Normalize the count matrices and set whether to use the Poisson KL divergence or the Frobenius normNormalizeCountMatrices
Create plots to help determine the number of latent factorsPlotLossvsLatentFactors
Generate UMAP plots for an object of class SickleJrPlotSickleJrUMAP
Run jrSiCKLSNMF on an object of class SickleJrRunjrSiCKLSNMF
Set lambda values and type of row regularization for an object of class SickleJrSetLambdasandRowReg
Set \mathbf{W} matrices and \mathbf{H} matrix from pre-calculated valuesSetWandHfromWHinitials
The SickleJr classSickleJr SickleJr-class
A simulated dataset for use with jrSiCKLSNMFSimData
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.SimSickleJrSmall