NoRCE

DOI: 10.18129/B9.bioc.NoRCE    

This is the development version of NoRCE; for the stable release version, see NoRCE.

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Bioconductor version: Development (3.12)

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.

Author: Gulden Olgun [aut, cre]

Maintainer: Gulden Olgun <gulden at cs.bilkent.edu.tr>

Citation (from within R, enter citation("NoRCE")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("NoRCE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NoRCE")

 

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Details

biocViews BiologicalQuestion, DifferentialExpression, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeAssembly, Software
Version 1.1.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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
LinkingTo
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
SystemRequirements
Enhances
URL
BugReports https://github.com/guldenolgun/NoRCE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package NoRCE_1.1.0.tar.gz
Windows Binary NoRCE_1.1.0.zip
macOS 10.13 (High Sierra) NoRCE_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NoRCE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NoRCE
Package Short Url https://bioconductor.org/packages/NoRCE/
Package Downloads Report Download Stats

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