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>.

Real-time quantitative polymerase chain reaction (qPCR) data
    sets by Karlen et al. (2007) <doi:10.1186/1471-2105-8-131>. Provides one
    single tabular tidy data set in long format, encompassing 32
    dilution series, for seven PCR targets and four biological samples. The
    targeted amplicons are within the murine genes: Cav1, Ccn2, Eln, Fn1, Rpl27,
    Hspg2, and Serpine1, respectively. Dilution series: scheme 1 (Cav1, Eln,
    Hspg2, Serpine1): 1-fold, 10-fold, 50-fold, and 100-fold; scheme 2 (Ccn2,
    Rpl27, Fn1): 1-fold, 10-fold, 50-fold, 100-fold and 1000-fold.
    For each concentration there are five replicates, except for the 1000-fold
    concentration, where only two replicates were performed. Each amplification
    curve is 40 cycles long. Original raw data file is Additional file 2 from
    "Statistical significance of quantitative PCR" by Y. Karlen, A. McNair,
    S. Perseguers, C. Mazza, and N. Mermod (2007)
    <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-8-131/MediaObjects/12859_2006_1503_MOESM2_ESM.ZIP>.

An R code with a GUI for microclimate time series, with an emphasis on underground environments. 'KarsTS' provides linear and nonlinear methods, including recurrence analysis (Marwan et al. (2007) <doi:10.1016/j.physrep.2006.11.001>) and filling methods (Moffat et al. (2007) <doi:10.1016/j.agrformet.2007.08.011>), as well as tools to manipulate easily time series and gap sets.