NoRCE
Bioc currentNoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
47 35 exported
Complexity
6.6 avg / 17 max
Call network
47 nodes / 106 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
8,055
Files
87
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
35
Internal functions
11
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
3
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-04-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
6
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 49
- Examples that run
- 26%10 run in a plain check · 28 never run
- Exported functions with examples
- 80%
- Documented parameters
- 95%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/guldenolgun/norce on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DER-18_TAD_adultbrain | data.frame | 2,734 × 3 | No other package |
| brain_disorder_ncRNA | data.frame | 1,363 × 1 | No other package |
| brain_mirna | data.frame | 407 × 1 | No other package |
| breastmRNA | data.frame | 667 × 1 | No other package |
| mirna | spec_tbl_df | 527 × 183 | No other package |
| mrna | data.frame | 527 × 150 | No other package |
| ncRegion | data.frame | 930 × 5 | No other package |
| tad_dmel | – | – | – |
| tad_hg19 | – | – | – |
| tad_hg38 | – | – | – |
| tad_mm10 | – | – | – |
Topics
People
- Gulden Olgun author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("NoRCE")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.