Package: jrSiCKLSNMF
Type: Package
Title: Clustering Single-Cell Multimodal Omics Data with Joint Graph
        Regularized Single-Cell Kullback-Leibler Sparse Non-Negative
        Matrix Factorization
Version: 2.0.0
Authors@R: 
    person("Dorothy","Ellis",,"ddemoreellis@gmail.com",role=c("aut","cre"),
    comment=c(ORCID="0000-0002-8624-0042"))
Maintainer: Dorothy Ellis <ddemoreellis@gmail.com>
Description: Methods to perform Joint graph Regularized Single-Cell
        Kullback-Leibler Sparse Non-negative Matrix Factorization
        (jrSiCKLSNMF, pronounced "junior sickles NMF") on quality
        controlled multi-assay single-cell omics count data,
        specifically dual-assay scRNA-seq and scATAC-seq data.
        'jrSiCKLSNMF' extracts meaningful latent factors that are
        shared across omics views. These factors enable accurate
        cell-type clustering, and facilitate visualizations. Also
        includes methods for mini- batch updates and other adaptations
        for larger datasets.
License: GPL-3 + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: Rcpp (>= 1.0.9), igraph, umap, kknn, ggplot2, methods, stats,
        rlang, Matrix,
        data.table,parallel,pbapply,cluster,MASS,clValid,factoextra,
        foreach,irlba,scran,purrr
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://ellisdoro.r-universe.dev
Date/Publication: 2024-06-10 07:25:17 UTC
RemoteUrl: https://github.com/ellisdoro/jrsicklsnmf
RemoteRef: HEAD
RemoteSha: c0c5253223e4d451d862dbf7991f0b8fde49707b
NeedsCompilation: yes
Packaged: 2026-06-16 07:08:26 UTC; root
Author: Dorothy Ellis [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8624-0042>)
Depends: R (>= 3.5.0)