cepip: Cell Explanatory Power with Inflection Point (CEP-IP) with CMRF

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>.

Version:	0.1.0
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
Published:	2026-10-29
DOI:	10.32614/CRAN.package.cepip (may not be active yet)
Author:	Kah Keng Wong [aut, cre]
Maintainer:	Kah Keng Wong <kahkeng3 at gmail.com>
BugReports:	https://github.com/kahkengwong/cepip/issues
License:	MIT + file LICENSE
URL:	https://github.com/kahkengwong/cepip
NeedsCompilation:	no
Materials:	NEWS
CRAN checks:	cepip results

Documentation:

Reference manual:	cepip.html , cepip.pdf
Vignettes:	Getting started with cepip (source, R code)

Downloads:

Package source:	cepip_0.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: cepip_0.1.0.zip, r-oldrel: not available
macOS binaries:	r-release (arm64): cepip_0.1.0.tgz, r-oldrel (arm64): cepip_0.1.0.tgz, r-release (x86_64): cepip_0.1.0.tgz, r-oldrel (x86_64): cepip_0.1.0.tgz

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