DOI: 10.18129/B9.bioc.NoRCE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see NoRCE.

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Bioconductor version: 3.16

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>

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


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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



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


biocViews BiologicalQuestion, DifferentialExpression, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeAssembly, Software
Version 1.10.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports KEGGREST, png, dplyr, graphics, RSQLite, DBI, tidyr, grDevices, stringr, GenomeInfoDb, S4Vectors, SummarizedExperiment, reactome.db, rWikiPathways, RCurl, dbplyr, utils, ggplot2, igraph, stats, reshape2, readr, GO.db, zlibbioc, biomaRt, rtracklayer, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi
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,,,,, BiocGenerics, org.Sc.sgd.db,,, methods, markdown
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_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64) NoRCE_1.10.0.tgz
macOS Binary (arm64) NoRCE_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: