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>.
Imports: Matrix, parallel, gaussquad, splines, scales, mvtnorm,
tmvtnorm, MASS, igraph, xtable, stringr, abind, expm, methods
Packaged: 2022-09-14 16:28:19 UTC; delcore.luca
Author: Luca Del Core [aut, cre, cph] (<https://orcid.org/0000-0002-1672-6995>),
Marco Grzegorczyk [aut, ths] (<https://orcid.org/0000-0002-2604-9270>),
Maintainer: Luca Del Core <l.del.core@rug.nl>

Title: An Interface for Karstic Time Series
Authors@R: c(person("Marina", "Saez", email = "marinasaez_andreu@hotmail.com",role = c("aut", "cre")),person("David", "Benavente", role = c("ths")),person("Soledad", "Cuezva", role = c("ths")),person("Concepcion", "Pla", role = c("ctb")))
Author: Marina Saez [aut, cre],  David Benavente [ths],  Soledad Cuezva [ths],  Concepcion Pla [ctb]
Description: An R graphical user interface for karstic time series, based on the 'tcltk' package. Karstic research typically includes CO2 and Rn concentrations and microclimatic measurements. Many of these time series have a strong non-linear behavior. Gaps are often a significant problem because caves are aggressive environments for the apparels. 'KarsTS' provides linear and non-linear analysis and filling methods, as well as tools to manipulate easily time series and gap sets.
Note: Please, cite this package as: Marina Saez (2017). KarsTS: An
Interface For Karstic Time Series. R package version 1.0.
Imports: circular, BaylorEdPsych, MVN, tcltk, tcltk2, tkrplot,
tseriesChaos, stlplus, tseries, forecast, stinepack,
missForest, nonlinearTseries, stats, graphics, utils, zoo,