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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "NoRCE" in publications use:'
type: software
license: MIT
title: 'NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment'
version: 1.17.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.NoRCE
abstract: '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.'
authors:
- family-names: Olgun
  given-names: Gulden
  email: gulden@cs.bilkent.edu.tr
preferred-citation:
  type: article
  title: 'NoRCE: Non-coding RNA sets cis enrichment tool'
  authors:
  - family-names: Olgun
    given-names: Gulden
    email: gulden@cs.bilkent.edu.tr
  - family-names: Nabi
    given-names: Afshan
  - family-names: Tastan
    given-names: Oznur
  journal: BMC bioinformatics
  year: '2021'
  publisher:
    name: BioMed Central
  start: 1-17
repository: https://bioc.r-universe.dev
repository-code: https://github.com/guldenolgun/NoRCE
commit: 421e9b899d99051335e817960a52d3aced056066
url: https://github.com/guldenolgun/NoRCE
contact:
- family-names: Olgun
  given-names: Gulden
  email: gulden@cs.bilkent.edu.tr