bioc-issue-bot
commented
6 years ago Hi @Jialab-UCR
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: GDCRNATools
Title: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Version: 0.99.0
Author: Ruidong Li,
Han Qu,
Shibo Wang,
Julong Wei,
Le Zhang,
Jianming Lu,
Zhenyu Jia
Maintainer: Ruidong Li <rli012@ucr.edu>,
Han Qu <hqu002@ucr.edu>
Description: This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression
data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer.
Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three
databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the
package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially
expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on
the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be
implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and
KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.
Depends: R (>= 3.3.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Imports: shiny,
jsonlite,
rjson,
XML,
limma,
edgeR,
DESeq2,
clusterProfiler,
DOSE,
org.Hs.eg.db,
biomaRt,
survival,
survminer,
pathview,
ggplot2,
gplots,
BiocParallel
Suggests: knitr,
testthat
VignetteBuilder: knitr
biocViews: GeneExpression, DifferentialExpression, GeneRegulation, GeneTarget,
NetworkInference, Survival, Visualization, GeneSetEnrichment,
NetworkEnrichment, Network, RNASeq, GO, KEGG
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-11-16 09:35:10 UTC; biocbuild
mtmorgan
Jialab-UCR
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