NoRCE
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see NoRCE.
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Bioconductor version: 3.12
While some non-coding RNAs (ncRNAs) have been found to play critical regulatory roles in biological processes, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs set needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together, and this spatial proximity hints at a functional association. Based on this idea, we present an R package, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out by using the functional annotations of the coding genes located proximally to the input ncRNAs. NoRCE allows incorporating other biological information such as the topologically associating domain (TAD) regions, co-expression patterns, and miRNA target information. NoRCE repository includes several data files, such as cell line specific TAD regions, functional gene sets, and cancer expression data. Additionally, users can input custom data files. Results can be retrieved in a tabular format or viewed as graphs. 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("NoRCE")):
Installation
To install this package, start R (version "4.0") 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")| Noncoding RNA Set Cis Annotation and Enrichment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, DifferentialExpression, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeAssembly, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/guldenolgun/NoRCE/issues |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NoRCE_1.2.0.tar.gz |
| Windows Binary | NoRCE_1.2.0.zip |
| macOS 10.13 (High Sierra) | NoRCE_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NoRCE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NoRCE |
| Bioc Package Browser | https://code.bioconductor.org/browse/NoRCE/ |
| Package Short Url | https://bioconductor.org/packages/NoRCE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |