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DESCRIPTION
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DESCRIPTION
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Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.2.0
Authors@R: c(
person("Julien", "Chiquet", role = c("aut", "cre"), email = "julien.chiquet@inrae.fr",
comment = c(ORCID = "0000-0002-3629-3429")),
person("Mahendra", "Mariadassou", role = "aut", email = "mahendra.mariadassou@inrae.fr",
comment = c(ORCID = "0000-0003-2986-354X")),
person("Stéphane", "Robin", role ="aut", email = "stephane.robin@inrae.fr"),
person("François", "Gindraud", role = "aut", email = "francois.gindraud@gmail.com"),
person("Julie", "Aubert", role = "ctb", email = "julie.aubert@inrae.fr"),
person("Bastien", "Batardière", role = "ctb", email = "bastien.batardiere@inrae.fr"),
person("Giovanni", "Poggiato", role = "ctb", email = "giov.poggiato@gmail.com"),
person("Cole", "Trapnell", role = "ctb", email = "coletrap@uw.edu"),
person("Maddy", "Duran", role = "ctb", email = "duran@uw.edu")
)
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin,
2021 <doi:10.3389/fevo.2021.588292>) can be used for
a variety of multivariate problems when count data are at play, including
principal component analysis for count data, discriminant analysis, model-based clustering and
network inference. Implements variational algorithms to fit such models accompanied with a set of
functions for visualization and diagnostic.
URL: https://pln-team.github.io/PLNmodels/
BugReports: https://github.com/pln-team/PLNmodels/issues
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends: R (>= 3.4)
LazyData: true
biocViews:
Imports:
methods,
stats,
MASS,
future,
future.apply,
R6,
glassoFast,
pscl,
Matrix,
Rcpp,
nloptr,
igraph,
grid,
gridExtra,
dplyr,
tidyr,
purrr,
ggplot2,
corrplot,
magrittr,
torch,
rlang
Suggests:
knitr,
rmarkdown,
testthat,
pkgdown,
spelling,
factoextra
LinkingTo: Rcpp, RcppArmadillo, nloptr
VignetteBuilder: knitr
Collate:
'PLNfit-class.R'
'PLN.R'
'PLNLDA.R'
'PLNLDAfit-S3methods.R'
'PLNLDAfit-class.R'
'PLNPCA.R'
'PLNPCAfamily-S3methods.R'
'PLNfamily-class.R'
'PLNPCAfamily-class.R'
'PLNPCAfit-S3methods.R'
'PLNPCAfit-class.R'
'PLNfamily-S3methods.R'
'PLNfit-S3methods.R'
'PLNmixture.R'
'PLNmixturefamily-S3methods.R'
'PLNmixturefamily-class.R'
'PLNmixturefit-S3methods.R'
'PLNmixturefit-class.R'
'PLNmodels-package.R'
'PLNnetwork.R'
'PLNnetworkfamily-S3methods.R'
'PLNnetworkfamily-class.R'
'PLNnetworkfit-S3methods.R'
'PLNnetworkfit-class.R'
'RcppExports.R'
'ZIPLNfit-class.R'
'ZIPLN.R'
'ZIPLNfit-S3methods.R'
'ZIPLNnetwork.R'
'barents.R'
'import_utils.R'
'mollusk.R'
'oaks.R'
'plot_utils.R'
'scRNA.R'
'trichoptera.R'
'utils-pipe.R'
'utils-zipln.R'
'utils.R'
'zzz.R'
Language: en-US