Package: circRNAprofiler 1.21.0

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_1.21.0.tar.gz
circRNAprofiler_1.21.0.zip(r-4.5)circRNAprofiler_1.21.0.zip(r-4.4)circRNAprofiler_1.21.0.zip(r-4.3)
circRNAprofiler_1.21.0.tgz(r-4.4-any)circRNAprofiler_1.21.0.tgz(r-4.3-any)
circRNAprofiler_1.21.0.tar.gz(r-4.5-noble)circRNAprofiler_1.21.0.tar.gz(r-4.4-noble)
circRNAprofiler_1.21.0.tgz(r-4.4-emscripten)circRNAprofiler_1.21.0.tgz(r-4.3-emscripten)
circRNAprofiler.pdf |circRNAprofiler.html✨
circRNAprofiler/json (API)
NEWS

# Install 'circRNAprofiler' in R:

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

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

Datasets:

ahChainFiles - AhChainFile
ahRepeatMasker - AhRepeatMasker
attractSpecies - AttractSpecies
backSplicedJunctions - BackSplicedJunctions
gtf - Gtf
gwasTraits - GwasTraits
iupac - Iupac
memeDB - MemeDB
mergedBSJunctions - MergedBSJunctions
miRspeciesCodes - MiRspeciesCodes

On BioConductor:circRNAprofiler-1.21.0(bioc 3.21)circRNAprofiler-1.20.0(bioc 3.20)

annotation structuralprediction functionalprediction geneprediction genomeassembly differentialexpression

5.78 score 10 stars 5 scripts 288 downloads 2 mentions 38 exports 133 dependencies

Last updated 2 months agofrom:1018c6c2a6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	NOTE	Dec 19 2024
R-4.4-mac	NOTE	Dec 19 2024
R-4.3-win	NOTE	Dec 19 2024
R-4.3-mac	NOTE	Dec 19 2024

Exports:annotateBSJs annotateRepeats annotateSNPsGWAS checkProjectFolder filterCirc formatGTF getBackSplicedJunctions getCircSeqs getDeseqRes getDetectionTools getEdgerRes getMiRsites getMotifs getRandomBSJunctions getRegexPattern getSeqsAcrossBSJs getSeqsFromGRs importCircExplorer2 importCircMarker importKnife importMapSplice importNCLscan importOther importUroborus initCircRNAprofiler liftBSJcoords mergeBSJunctions mergeMotifs plotExBetweenBSEs plotExPosition plotHostGenes plotLenBSEs plotLenIntrons plotMiR plotMotifs plotTotExons rearrangeMiRres volcanoPlot

Dependencies:abind ade4 AnnotationDbi AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg19 cachem cli clipr codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 dplyr edgeR fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable gwascat hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pixmap pkgconfig plogr plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppThread RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales segmented seqinr snow snpStats sp SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils universalmotif utf8 VariantAnnotation vctrs viridisLite vroom withr XML XVector yaml zlibbioc

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

Simona Aufiero

Rendered fromcircRNAprofiler.Rmdusingknitr::rmarkdownon Dec 19 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ahChainFile	ahChainFiles
ahRepeatMasker	ahRepeatMasker
Annotate circRNA features.	annotateBSJs
Annotate repetitive elements	annotateRepeats
Annotate GWAS SNPs	annotateSNPsGWAS
attractSpecies	attractSpecies
backSplicedJunctions	backSplicedJunctions
Check project folder	checkProjectFolder
Filter circRNAs	filterCirc
Format annotation file	formatGTF
Import detected circRNAs	getBackSplicedJunctions
Retrieve circRNA sequences	getCircSeqs
Differential circRNA expression analysis adapted from DESeq2	getDeseqRes
Create data frame with circRNA detection codes	getDetectionTools
Differential circRNA expression analysis adapted from EdgeR	getEdgerRes
Screen target sequences for miR binding sites	getMiRsites
Screen target sequences for recurrent motifs	getMotifs
Retrieve random back-spliced junctions	getRandomBSJunctions
Convert IUPAC sequence to an regular expression	getRegexPattern
Retrieve back-spliced junction sequences	getSeqsAcrossBSJs
Retrieve sequences flanking back-spliced junctions	getSeqsFromGRs
gtf	gtf
gwasTraits	gwasTraits
Initialize the project folder	initCircRNAprofiler
iupac	iupac
LiftOver back-spliced junction coordinates	liftBSJcoords
memeDB	memeDB
Group circRNAs identified by multiple prediction tools	mergeBSJunctions
mergedBSJunctions	mergedBSJunctions
Group motifs shared by multiple RBPs	mergeMotifs
miRspeciesCodes	miRspeciesCodes
Plot exons between back-spliced junctions	plotExBetweenBSEs
Plot back-spliced exon positions	plotExPosition
Plot circRNA host genes	plotHostGenes
Plot length back-spliced exons	plotLenBSEs
Plot length introns flanking back-spliced junctions	plotLenIntrons
Plot miRNA analysis results	plotMiR
Plot motifs analysis results	plotMotifs
Plot exons in the circRNA host transcript	plotTotExons
Rearrange miR results	rearrangeMiRres
Plot differential circRNA expression results	volcanoPlot