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:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=cepip
to link to this page.