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scModels
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]
[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
Previous versions and publish date:
Other packages that cited scModels R package
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Other R packages that scModels depends,
imports, suggests or enhances
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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