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 (3.15)

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>

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

Installation

To install this package, start R (version "4.2") 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 1.7.1
In Bioconductor since BioC 3.11 (R-4.0) (1.5 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
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Build Report  

Package Archives

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

Source Package NoRCE_1.7.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) NoRCE_1.7.1.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/
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