bioc-issue-bot
commented
1 year ago Hi @habilzare
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: iNETgrate
Type: Package
Title: Integrates DNA methylation data with gene expression in a single gene network
Version: 0.99.12
Date: 2022-06-01
Authors@R: c(
person("Isha", "Mehta", role = "aut",
comment = c(ORCID = "0000-0002-6009-0787")),
person("Ghazal", "Ebrahimi", role = "aut"),
person("Hanie", "Samimi", role = "aut"),
person("Habil", "Zare", email = "zare@u.washington.edu",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5902-6238")))
biocViews: GeneExpression, RNASeq, DNAMethylation,
NetworkInference, Network, GraphAndNetwork, BiomedicalInformatics,
SystemsBiology, Transcriptomics, Classification, Clustering,
DimensionReduction, PrincipalComponent, mRNAMicroarray,
Normalization, GenePrediction, KEGG, Survival
Depends: R (>= 3.5.0), BiocStyle (>= 2.18.1)
Description: The iNETgrate package provides functions to build a correlation network in which nodes
are genes. DNA methylation and gene expression data are integrated to define the
connections between genes. This network is used to identify modules (clusters) of
genes. The biological information in each of the resulting modules is represented by an
eigengene. These biological signatures can be used as features e.g., for classification
of patients into risk categories. The resulting biological signatures are very robust
and give a holistic view of the underlying molecular changes.
Imports: SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA, grDevices,
graphics, survival, igraph, Pigengene (>= 1.19.26), Homo.sapiens, glmnet,
caret, gplots, minfi, TCGAbiolinks, matrixStats, Rfast, tidyr, tidyselect, utils
Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19,
AnnotationDbi
License: GPL-3
BugReports: https://github.com/Bioconductor/BiocManager/issues
VignetteBuilder: knitr
NeedsCompilation: no
vjcitn
habilzare
nilseling
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