Package: NoRCE
Type: Package
Title: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Version: 1.0.0
Authors@R: c(person("Gulden", "Olgun", 
           email = "gulden@cs.bilkent.edu.tr", 
		   role = c("aut", "cre")))
Description: While some non-coding RNAs (ncRNAs) have been found to 
  play critical regulatory roles in biological processes, most remain 
  functionally uncharacterized. This presents a challenge whenever an
  interesting set of ncRNAs set needs to be analyzed in a functional 
  context. Transcripts located close-by on the genome are often regulated
  together, and this spatial proximity hints at a functional association.
  Based on this idea, we present an R package, NoRCE, that performs cis
  enrichment analysis for a given set of ncRNAs. Enrichment is carried
  out by using the functional annotations of the coding genes located
  proximally to the input ncRNAs. NoRCE allows incorporating other biological 
  information such as the topologically associating domain (TAD) regions, 
  co-expression patterns, and miRNA target information. NoRCE repository
  includes several data files, such as cell line specific TAD regions, 
  functional gene sets, and cancer expression data. Additionally, users
  can input custom data files. Results can be retrieved in a tabular
  format or viewed as graphs. NoRCE is currently available for the following
  species: human, mouse, rat, zebrafish, fruit fly, worm and yeast. 
License: MIT + file LICENSE
Depends: R (>= 4.0)
Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,
        S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl,
        dbplyr,utils,ggplot2,igraph,stats,reshape2,readr,
        GO.db,zlibbioc,
        biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi
Encoding: UTF-8
RoxygenNote: 7.0.2
Suggests: knitr,
        TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown,
        TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene,
        org.Mm.eg.db,
        org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics,
        org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,
VignetteBuilder: knitr
biocViews: BiologicalQuestion, DifferentialExpression,
        GenomeAnnotation, GeneSetEnrichment, GeneTarget,
        GenomeAssembly, GO
LazyData: true
BugReports: https://github.com/guldenolgun/NoRCE/issues
git_url: https://git.bioconductor.org/packages/NoRCE
git_branch: RELEASE_3_11
git_last_commit: bda1f3d
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 04:45:04 UTC; biocbuild
Author: Gulden Olgun [aut, cre]
Maintainer: Gulden Olgun <gulden@cs.bilkent.edu.tr>
Built: R 4.0.0; ; 2020-05-13 10:53:44 UTC; unix
