Package: cepip
Type: Package
Title: Cell Explanatory Power with Inflection Point (CEP-IP) with CMRF
Version: 0.1.0
Authors@R: 
    person("Kah Keng", "Wong", role = c("aut", "cre"),
           email = "kahkeng3@gmail.com",
           comment = c(ORCID = "0000-0001-7359-6202"))
Description: Implements the cell explanatory power with inflection point
    (CEP-IP) framework for single-cell co-expression analysis. A generalized
    additive model (GAM) fitted by restricted maximum likelihood (REML) with
    a penalized residual sum of squares (PRSS) search over the basis
    dimension relates a gene of interest to the mean of its partner genes.
    Cells are ranked by their explanatory power, and the inflection point is
    the first negative-to-positive zero crossing of a residual GAM. Optional
    extensions are the Spearman-Kendall cell-level score (SKCS) and the
    copula monotone recovery filter (CMRF), which recovers cells near the
    module through a tolerance band and a repeated stratified k-fold
    cross-validation gate. Downstream helpers give per-donor module
    fractions, paired donor-level differential expression and donor-level
    association models. CEP-IP is described in Wong (2026)
    <doi:10.1016/j.cmpb.2026.109372>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1.0)
Imports: mgcv, stats, utils, methods, grDevices, grid, parallel,
        Matrix, ggplot2 (>= 3.4.0), gridExtra, openxlsx
Suggests: Hmisc, energy, clinfun, pcaPP, testthat (>= 3.0.0), knitr,
        rmarkdown
VignetteBuilder: knitr
Config/testthat/edition: 3
RoxygenNote: 7.3.1
URL: https://github.com/kahkengwong/cepip
BugReports: https://github.com/kahkengwong/cepip/issues
NeedsCompilation: no
Packaged: 2026-10-19 23:24:38 UTC; root
Author: Kah Keng Wong [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7359-6202>)
Maintainer: Kah Keng Wong <kahkeng3@gmail.com>
Repository: CRAN
Date/Publication: 2026-10-29 19:30:19 UTC
Built: R 4.5.2; ; 2026-10-29 21:07:56 UTC; unix
