Package: NoRCE 1.17.0

Gulden Olgun

NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

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:Gulden Olgun [aut, cre]

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NoRCE.pdf |NoRCE.html✨
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NEWS

# Install 'NoRCE' in R:
install.packages('NoRCE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/guldenolgun/norce/issues

Datasets:
  • brain_disorder_ncRNA - Differentially expressed non-coding gene
  • brain_mirna - Differentially expressed human brain data
  • breastmRNA - Protein coding genes that are differentially expressed in TCGA breast cancer RNAseq data.
  • mirna - Brain miRNA expression retrieved from the TCGA
  • mrna - Brain mRNA expression retrieved from the TCGA
  • ncRegion - Differentially expressed non-coding gene regions
  • tad_dmel - TAD regions for the fly
  • tad_hg19 - TAD regions for human hg19 assembly
  • tad_hg38 - TAD regions for human hg38 assembly
  • tad_mm10 - TAD regions for mouse

On BioConductor:NoRCE-1.17.0(bioc 3.20)NoRCE-1.16.0(bioc 3.19)

bioconductor-package

35 exports 0.61 score 119 dependencies 2 mentions

Last updated 2 months agofrom:421e9b899d

Exports:assemblycalculateCorrconvertGeneIDconvertGMTcorrbasedcorrbasedMrnacreateNetworkdrawDotPlotextractBiotypefilterBiotypegeneGOEnrichergenePathwayEnrichergeneRegionGOEnrichergeneRegionPathwayEnrichergetGoDaggetKeggDiagramgetmiRNACountgetNearToExongetNearToIntrongetReactomeDiagramgetTADOverlapgetUCSCgoEnrichmentKeggEnrichmentlistTADmirnaGOEnrichermirnaPathwayEnrichermirnaRegionGOEnrichermirnaRegionPathwayEnricherpredictmiTargetsreactomeEnrichmentsetParameterstopEnrichmentWikiEnrichmentwriteEnrichment

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgtablehmshttrhttr2igraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreactome.dbreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerrWikiPathwaysS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2XVectoryamlzlibbioc

NoRCE: Noncoding RNA Set Cis Annotation and Enrichment

Rendered fromNoRCE.Rmdusingknitr::knitron Jun 18 2024.

Last update: 2022-10-18
Started: 2019-05-26

Readme and manuals

Help Manual

Help pageTopics
Annotate the set of genes with the GO terms for a given species and assemblyannGO
Get the required information for the given assemblyassembly
Differentially expressed non-coding genebrain_disorder_ncRNA
Differentially expressed human brain databrain_mirna
Protein coding genes that are differentially expressed in TCGA breast cancer RNAseq data.breastmRNA
Calculates the correlation coefficient values between two custom expression data.calculateCorr
Convert gene ids according to the gene typeconvertGeneID
Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol formatted data frameconvertGMT
Pearson correlation coefficient value of the miRNA genes between miRNA:mRNA for a given correlation cut-off and cancer.corrbased
Pearson correlation coefficient value of the mRNA genes between miRNA:mRNA for a given correlation cut-off and cancer.corrbasedMrna
Create interaction network for top n enriched GO term:coding RNA or GO-term:noncoding RNA interaction. Nodes are GO term and RNA, edges are interactions between them. Each GO-term is annotated and enriched with the mRNAs provided from the input list.createNetwork
Draw dot plot of the enrichment objectdrawDotPlot
Get the biotype of the non-coding genes. It is suitable for the GENCODE gtf filesextractBiotype
Extract the genes that have user provided biotypes. This method is useful when input gene list is mixed or when research of the interest is only focused on specific group of genes.filterBiotype
Given genes that fall in a given upstream and downstream region of mRNAs of interest, GO term enrichment analysis is carried outgeneGOEnricher
Given genes that fall in the given upstream and downstream region of mRNAs of interest, pathway enrichment analysis is carried outgenePathwayEnricher
Given gene regions that fall in the given upstream and downstream region of mRNAs of interest, GO term enrichment analysis is carried outgeneRegionGOEnricher
Given gene regions that fall in the given upstream and downstream region of mRNAs of interest, pathway enrichment analysis is carried outgeneRegionPathwayEnricher
Plot and save the GO term DAG of the top n enrichments in terms of p-values or adjusted p-values with an user provided formatgetGoDag
Display the enriched KEGG diagram of the KEGG pathway. This function is specific to only one KEGG pathway id and identifies the enriched genes in the diagram.getKeggDiagram
Get TCGA miRNAseq expression of miRNA genes for the given cancergetmiRNACount
Get only those neighbouring genes that fall within exon regiongetNearToExon
Get only those neighbouring genes that fall within intron regiongetNearToIntron
Display the enriched Reactome diagram of the given Reactome pathway id. This function is specific to only one pathway id and identifies the enriched genes in the diagram.getReactomeDiagram
For given region of interest, overlapped genes in the TAD regions are found. Results can be filtered according to the available cell lines.getTADOverlap
Get nearest genes for the window of the upstream/downstream region.getUCSC
Perform enrichment analysis of the given genesgoEnrichment
KEGG pathway enrichmentKeggEnrichment
List cell line of the given topological domain regionslistTAD
Brain miRNA expression retrieved from the TCGAmirna
GO term enrichments of the microRNA genes with mRNAs that fall in the given upstream/downstream regions of the microRNA genesmirnaGOEnricher
Pathway enrichments of the microRNA genes with mRNAs that fall in the given upstream/downstream regions of the microRNA genesmirnaPathwayEnricher
GO enrichments of the microRNA regions with mRNAs that fall in the given upstream/downstream regions of the microRNA genesmirnaRegionGOEnricher
Pathway enrichments of the microRNA regions with mRNAs that fall in the given upstream/downstream regions of the microRNA genesmirnaRegionPathwayEnricher
Brain mRNA expression retrieved from the TCGAmrna
Differentially expressed non-coding gene regionsncRegion
An S4 class to represent enrichmentNoRCE-class
Check the package availability for the given assemblypackageCheck
For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.pathwayEnrichment
Predict the miRNA targets for the miRNA or mRNA genes, which is specified with type parameterpredictmiTargets
Reactome pathway enrichmentreactomeEnrichment
Set the parameterssetParameters
TAD regions for the flytad_dmel
TAD regions for human hg19 assemblytad_hg19
TAD regions for human hg38 assemblytad_hg38
TAD regions for mousetad_mm10
Number of top enrichment results of the pathway or GO terms for the given object and the order type - p-value or adjusted p-value.topEnrichment
WikiPathways EnrichmentWikiEnrichment
Write the tabular form of the pathway or GO term enrichment resultswriteEnrichment