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scModels  

Fitting Discrete Distribution Models to Count Data
View on CRAN: Click here


Download and install scModels package within the R console
Install from CRAN:
install.packages("scModels")

Install from Github:
library("remotes")
install_github("cran/scModels")

Install by package version:
library("remotes")
install_version("scModels", "1.0.4")



Attach the package and use:
library("scModels")
Maintained by
Lisa Amrhein
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-06-13
Latest Update: 2023-01-24
Description:
Provides functions for fitting discrete distribution models to count data. Included are the Poisson, the negative binomial, the Poisson-inverse gaussian and, most importantly, a new implementation of the Poisson-beta distribution (density, distribution and quantile functions, and random number generator) together with a needed new implementation of Kummer's function (also: confluent hypergeometric function of the first kind). Three different implementations of the Gillespie algorithm allow data simulation based on the basic, switching or bursting mRNA generating processes. Moreover, likelihood functions for four variants of each of the three aforementioned distributions are also available. The variants include one population and two population mixtures, both with and without zero-inflation. The package depends on the 'MPFR' libraries () which need to be installed separately (see description at ). This package is supplement to the paper "A mechanistic model for the negative binomial distribution of single-cell mRNA counts" by Lisa Amrhein, Kumar Harsha and Christiane Fuchs (2019) available on bioRxiv.
How to cite:
Lisa Amrhein (2019). scModels: Fitting Discrete Distribution Models to Count Data. R package version 1.0.4, https://cran.r-project.org/web/packages/scModels. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2019-06-13 18:10), 1.0.1 (2019-09-03 02:00), 1.0.2 (2021-02-26 15:10), 1.0.3 (2022-03-29 23:50)
Other packages that cited scModels R package
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Other R packages that scModels depends, imports, suggests or enhances
Complete documentation for scModels
Functions, R codes and Examples using the scModels R package
Some associated functions: Inverse-Gaussian . Poisson-beta . chf_1F1 . fit_params . gmRNA . nlogL . 
Some associated R codes: RcppExports.R . gillespie.R . log_likelihood.R . par_est_fns.R . pb.R .  Full scModels package functions and examples
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