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DESCRIPTION
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DESCRIPTION
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Package: BioNERO
Type: Package
Title: Biological Network Reconstruction Omnibus
Version: 1.5.2
Authors@R: c(person("Fabricio", "Almeida-Silva",
email="[email protected]",
role=c("cre", "aut"),
comment = c(ORCID = "0000-0002-5314-2964")),
person("Thiago", "Venancio",
role="aut",
comment = c(ORCID = "0000-0002-2215-8082")))
Description: BioNERO aims to integrate all aspects of biological network inference
in a single package, including data preprocessing, exploratory analyses,
network inference, and analyses for biological interpretations. BioNERO
can be used to infer gene coexpression networks (GCNs) and gene
regulatory networks (GRNs) from gene expression data. Additionally,
it can be used to explore topological properties of protein-protein
interaction (PPI) networks. GCN inference relies on the popular WGCNA
algorithm. GRN inference is based on the "wisdom of the crowds" principle,
which consists in inferring GRNs with multiple algorithms (here, CLR,
GENIE3 and ARACNE) and calculating the average rank for each interaction
pair. As all steps of network analyses are included in this package,
BioNERO makes users avoid having to learn the syntaxes of several
packages and how to communicate between them. Finally, users can also
identify consensus modules across independent expression sets and
calculate intra and interspecies module preservation statistics
between different networks.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: false
URL: https://github.com/almeidasilvaf/BioNERO
BugReports: https://github.com/almeidasilvaf/BioNERO/issues
biocViews:
Software,
GeneExpression,
GeneRegulation,
SystemsBiology,
GraphAndNetwork,
Preprocessing,
Network
Imports:
WGCNA,
dynamicTreeCut,
matrixStats,
sva,
RColorBrewer,
ComplexHeatmap,
ggplot2,
ggrepel,
patchwork,
reshape2,
igraph,
ggnetwork,
intergraph,
networkD3,
ggnewscale,
NetRep,
stats,
grDevices,
graphics,
utils,
methods,
BiocParallel,
minet,
GENIE3,
SummarizedExperiment
RoxygenNote: 7.2.0
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0),
BiocStyle,
DESeq2,
covr
VignetteBuilder: knitr
Config/testthat/edition: 3