c(
person(given = "Sophie", family = "Donnet", role = c("aut", "cre"), email = "sophie.donnet@inrae.fr", comment = c(ORCID = "0000-0003-4370-7316")),
person(given = "Pierre", family = "Barbillon", role = c("aut"), email = "pierre.barbillon@agroparistech.fr",comment = c(ORCID = "0000-0002-7766-7693"))
)
We define generalized multipartite networks  as the joint observation of several networks implying some common pre-specified groups of individuals. The aim is to fit an adapted version of  the popular stochastic block model to multipartite networks, as described in Bar-hen, Barbillon and Donnet (2020) <arXiv:1807.10138>.
testthat (>= 2.1.0), spelling, knitr, rmarkdown
R6, parallel, grDevices, graphics, stats, utils, igraph,
mclust, blockmodels, aricode, pbmcapply
'GREMLINS_package.R' 'BMPOO.R' 'defineNetwork.R'
'multipartiteBM.R' 'VEMPOOVersion.R'
'multipartiteBMFixedModel.R' 'initializeVEM.R' 'plotMBM.R'
'searchVKPOOVersion.R' 'utils.R' 'compLikICL.R'
'extractClustersMBM.R' 'rMBM.R' 'comparClassif.R'
'MPEcoNetwork.R' 'predictMBM.R'
Sophie Donnet [aut, cre] (<https://orcid.org/0000-0003-4370-7316>),
Pierre Barbillon [aut] (<https://orcid.org/0000-0002-7766-7693>)

GEO RNA-Seq Experiments Processing Pipeline
c(person("Naim Al", "Mahi", role = c("cre", "aut"),
email = "mahina@mail.uc.edu"),
person("Mario", "Medvedovic", role = c("aut", "ctb")))
An R based pipeline to download and process Gene Expression Omnibus (GEO) RNA-seq data.
For a given GEO series accession ID, this pipeline generates metadata,
both gene and transcript level counts, and quality control (QC) report.
XML, rentrez, RCurl, GEOquery, Biobase, parallel, tximport,
EnsDb.Hsapiens.v86, EnsDb.Rnorvegicus.v79, EnsDb.Mmusculus.v79,
AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
GenomicFeatures, utils
SRAtoolkit, Salmon, Java, FastQC, MultiQC
Naim Al Mahi [cre, aut],
Mario Medvedovic [aut, ctb]

An R based pipeline to download and process Gene Expression Omnibus (GEO) RNA-seq data.
For a given GEO series accession ID, this pipeline generates metadata,
both gene and transcript level counts, and quality control (QC) report.
This package is mainly developed to process the GEO RNA-seq datasets
for the web platform GREIN. More details about GREP2 and GREIN can be
found here <doi:10.1101/326223>.