Karen: Kalman Reaction Networks

This is a stochastic framework that combines biochemical reaction networks with extended Kalman filter and Rauch-Tung-Striebel smoothing. This framework allows to investigate the dynamics of cell differentiation from high-dimensional clonal tracking data subject to measurement noise, false negative errors, and systematically unobserved cell types. Our tool can provide statistical support to biologists in gene therapy clonal tracking studies for a deeper understanding of clonal reconstitution dynamics. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.07.08.499353>.

Version: 1.0
Depends: R (≥ 2.10)
Imports: Matrix, parallel, gaussquad, splines, scales, mvtnorm, tmvtnorm, MASS, igraph, xtable, stringr, abind, expm, methods
Suggests: R.rsp
Published: 2022-09-15
DOI: 10.32614/CRAN.package.Karen
Author: Luca Del Core ORCID iD [aut, cre, cph], Danilo Pellin ORCID iD [aut], Marco Grzegorczyk ORCID iD [aut, ths], Ernst Wit ORCID iD [aut, ths]
Maintainer: Luca Del Core <l.del.core at rug.nl>
License: GPL-3
NeedsCompilation: no
CRAN checks: Karen results


Reference manual: Karen.pdf
Vignettes: Using Karen


Package source: Karen_1.0.tar.gz
Windows binaries: r-devel: Karen_1.0.zip, r-release: Karen_1.0.zip, r-oldrel: Karen_1.0.zip
macOS binaries: r-release (arm64): Karen_1.0.tgz, r-oldrel (arm64): Karen_1.0.tgz, r-release (x86_64): Karen_1.0.tgz, r-oldrel (x86_64): Karen_1.0.tgz


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