Package: scLANE
Type: Package
Title: Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs,
        & GLMMs
Version: 1.1.1
Authors@R: c(person(given = c("Jack", "R."), family = "Leary", email = "j.leary@ufl.edu", role = c("aut", "cre"), comment = c(ORCID = "0009-0004-8821-3269")), 
             person(given = "Rhonda", family = "Bacher", email = "rbacher@ufl.edu", role = c("ctb", "fnd"), comment = c(ORCID = "0000-0001-5787-476X")))
Description: Our scLANE model uses truncated power basis spline models
        to build flexible, interpretable models of single cell gene
        expression over pseudotime or latent time. The modeling
        architectures currently supported are Negative-binomial GLMs,
        GEEs, & GLMMs. Downstream analysis functionalities include
        model comparison, dynamic gene clustering, smoothed counts
        generation, gene set enrichment testing, & visualization.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: glm2, magrittr, R (>= 4.4.0)
Imports: geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr,
        furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2,
        splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr,
        tidyselect, broom.mixed, Rcpp
URL: https://github.com/jr-leary7/scLANE
BugReports: https://github.com/jr-leary7/scLANE/issues
Suggests: covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba,
        rlang, magick, igraph, scater, gtable, ggpubr, viridis,
        bluster, cluster, circlize, speedglm, rmarkdown, gridExtra,
        BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel,
        BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0),
        testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment
VignetteBuilder: knitr
Config/testthat/edition: 3
LinkingTo: Rcpp, RcppEigen
biocViews: RNASeq, Software, Clustering, TimeCourse, Sequencing,
        Regression, SingleCell, Visualization, GeneExpression,
        Transcriptomics, GeneSetEnrichment, DifferentialExpression
Additional_repositories: https://bioconductor.org/packages/release/bioc
Config/pak/sysreqs: cmake make libicu-dev libssl-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-12-16 21:08:34 UTC
RemoteUrl: https://github.com/bioc/scLANE
RemoteRef: HEAD
RemoteSha: e2002e76e9e91eb0a7e4ec68a5d08ed997ed4173
NeedsCompilation: yes
Packaged: 2025-12-17 04:00:51 UTC; root
Author: Jack R. Leary [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-8821-3269>),
  Rhonda Bacher [ctb, fnd] (ORCID:
    <https://orcid.org/0000-0001-5787-476X>)
Maintainer: Jack R. Leary <j.leary@ufl.edu>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-12-17 04:04:56 UTC; windows
Archs: x64
