NoRCE

DOI: 10.18129/B9.bioc.NoRCE    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see NoRCE.

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Bioconductor version: 3.14

While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. 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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	Noncoding RNA Set Cis Annotation and Enrichment
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiologicalQuestion, DifferentialExpression, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeAssembly, Software
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
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, markdown
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_1.6.0.tar.gz
Windows Binary	NoRCE_1.6.0.zip
macOS 10.13 (High Sierra)	NoRCE_1.6.0.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