Package: Karen
Title: Kalman Reaction Networks
Version: 1.0
Authors@R: 
    c(person(given = "Luca", 
            family = "Del Core", 
            email = "l.del.core@rug.nl", 
            role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-1672-6995")),
    person(given = "Danilo", 
            family = "Pellin", 
            email = "Danilo_Pellin@DFCI.HARVARD.EDU", 
            role = c("aut"),
            comment = c(ORCID = "0000-0002-2647-0508")),
    person(given = "Marco", 
            family = "Grzegorczyk", 
            email = "m.a.grzegorczyk@rug.nl", 
            role = c("aut", "ths"),
            comment = c(ORCID = "0000-0002-2604-9270")),
    person(given = "Ernst", 
            family = "Wit", 
            email = "ernst.jan.camiel.wit@usi.ch", 
            role = c("aut", "ths"),
            comment = c(ORCID = "0000-0002-3671-9610")))
Description: 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>.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.2
Imports: Matrix, parallel, gaussquad, splines, scales, mvtnorm,
        tmvtnorm, MASS, igraph, xtable, stringr, abind, expm, methods
Depends: R (>= 2.10)
LazyData: true
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-09-14 16:28:19 UTC; delcore.luca
Author: Luca Del Core [aut, cre, cph] (<https://orcid.org/0000-0002-1672-6995>),
  Danilo Pellin [aut] (<https://orcid.org/0000-0002-2647-0508>),
  Marco Grzegorczyk [aut, ths] (<https://orcid.org/0000-0002-2604-9270>),
  Ernst Wit [aut, ths] (<https://orcid.org/0000-0002-3671-9610>)
Maintainer: Luca Del Core <l.del.core@rug.nl>
Repository: CRAN
Date/Publication: 2022-09-15 07:40:02 UTC
Built: R 4.6.0; ; 2026-04-26 04:01:25 UTC; unix
