Package: circRNAprofiler 1.26.0

Simona Aufiero

circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

Authors:Simona Aufiero

circRNAprofiler_1.26.0.tar.gz
circRNAprofiler_1.26.0.zip(r-4.7)circRNAprofiler_1.26.0.zip(r-4.6)circRNAprofiler_1.26.0.zip(r-4.5)
circRNAprofiler_1.26.0.tgz(r-4.6-any)circRNAprofiler_1.26.0.tgz(r-4.5-any)
circRNAprofiler_1.26.0.tar.gz(r-4.7-any)circRNAprofiler_1.26.0.tar.gz(r-4.6-any)
circRNAprofiler_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
circRNAprofiler/json (API)
NEWS

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

Bug tracker:https://github.com/aufiero/circrnaprofiler/issues

Datasets:

On BioConductor:circRNAprofiler-1.27.0(bioc 3.24)circRNAprofiler-1.26.0(bioc 3.23)

annotationstructuralpredictionfunctionalpredictiongenepredictiongenomeassemblydifferentialexpression

5.86 score 12 stars 6 scripts 470 downloads 2 mentions 38 exports 132 dependencies

Last updated from:ec74a823e2 (on RELEASE_3_23). Checks:6 ERROR, 2 OK, 2 NOTE. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR454
linux-devel-x86_64ERROR816
source / vignettesOK572
linux-release-x86_64ERROR829
macos-release-arm64NOTE620
macos-oldrel-arm64NOTE523
windows-develERROR746
windows-releaseERROR775
windows-oldrelERROR929
wasm-releaseOK397

Exports:annotateBSJsannotateRepeatsannotateSNPsGWAScheckProjectFolderfilterCircformatGTFgetBackSplicedJunctionsgetCircSeqsgetDeseqResgetDetectionToolsgetEdgerResgetMiRsitesgetMotifsgetRandomBSJunctionsgetRegexPatterngetSeqsAcrossBSJsgetSeqsFromGRsimportCircExplorer2importCircMarkerimportKnifeimportMapSpliceimportNCLscanimportOtherimportUroborusinitCircRNAprofilerliftBSJcoordsmergeBSJunctionsmergeMotifsplotExBetweenBSEsplotExPositionplotHostGenesplotLenBSEsplotLenIntronsplotMiRplotMotifsplotTotExonsrearrangeMiRresvolcanoPlot

Dependencies:abindade4AnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg19cachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2dplyredgeRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegwascathmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpixmappkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppThreadRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalessegmentedSeqinfoseqinrsnowsnpStatsspSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsuniversalmotifutf8VariantAnnotationvctrsviridisLitevroomwithrXMLXVectoryaml

circRNAprofiler: An R-based computational framework for the downstream analysis of circular RNAs

Simona Aufiero

Rendered fromcircRNAprofiler.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2023-10-13
Started: 2019-05-10

Readme and manuals

Help Manual

Help pageTopics
ahChainFileahChainFiles
ahRepeatMaskerahRepeatMasker
Annotate circRNA features.annotateBSJs
Annotate repetitive elementsannotateRepeats
Annotate GWAS SNPsannotateSNPsGWAS
attractSpeciesattractSpecies
backSplicedJunctionsbackSplicedJunctions
Check project foldercheckProjectFolder
Filter circRNAsfilterCirc
Format annotation fileformatGTF
Import detected circRNAsgetBackSplicedJunctions
Retrieve circRNA sequencesgetCircSeqs
Differential circRNA expression analysis adapted from DESeq2getDeseqRes
Create data frame with circRNA detection codesgetDetectionTools
Differential circRNA expression analysis adapted from EdgeRgetEdgerRes
Screen target sequences for miR binding sitesgetMiRsites
Screen target sequences for recurrent motifsgetMotifs
Retrieve random back-spliced junctionsgetRandomBSJunctions
Convert IUPAC sequence to an regular expressiongetRegexPattern
Retrieve back-spliced junction sequencesgetSeqsAcrossBSJs
Retrieve sequences flanking back-spliced junctionsgetSeqsFromGRs
gtfgtf
gwasTraitsgwasTraits
Initialize the project folderinitCircRNAprofiler
iupaciupac
LiftOver back-spliced junction coordinatesliftBSJcoords
memeDBmemeDB
Group circRNAs identified by multiple prediction toolsmergeBSJunctions
mergedBSJunctionsmergedBSJunctions
Group motifs shared by multiple RBPsmergeMotifs
miRspeciesCodesmiRspeciesCodes
Plot exons between back-spliced junctionsplotExBetweenBSEs
Plot back-spliced exon positionsplotExPosition
Plot circRNA host genesplotHostGenes
Plot length back-spliced exonsplotLenBSEs
Plot length introns flanking back-spliced junctionsplotLenIntrons
Plot miRNA analysis resultsplotMiR
Plot motifs analysis resultsplotMotifs
Plot exons in the circRNA host transcriptplotTotExons
Rearrange miR resultsrearrangeMiRres
Plot differential circRNA expression resultsvolcanoPlot