This is the development version of NoRCE; for the stable release version, see NoRCE.
NoRCE: Noncoding RNA Sets Cis Annotation and EnrichmentBioconductor version: Development (3.22)
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, entercitation("NoRCE")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("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 Details biocViews BiologicalQuestion, DifferentialExpression, GO, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeAssembly, Software Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 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 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, markdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package ArchivesFollow Installation instructions to use this package in your R session.
Source Package Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) 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/ Package Downloads Report Download StatsRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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