circRNAprofiler

This is the released version of circRNAprofiler; for the devel version, see circRNAprofiler.

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

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DOI: 10.18129/B9.bioc.circRNAprofiler

Bioconductor version: Release (3.22)

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.

Author: Simona Aufiero

Maintainer: Simona Aufiero <simo.aufiero at gmail.com>

Citation (from within R, enter citation("circRNAprofiler")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("circRNAprofiler")

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("circRNAprofiler")

circRNAprofiler HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License GPL-3

Depends R (>= 4.5.0)

Imports dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome

System Requirements

URL https://github.com/Aufiero/circRNAprofiler

Bug Reports https://github.com/Aufiero/circRNAprofiler/issues

Suggests testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package circRNAprofiler_1.24.0.tar.gz

Windows Binary (x86_64) circRNAprofiler_1.23.1.zip (64-bit only)

macOS Binary (x86_64) circRNAprofiler_1.24.0.tgz

macOS Binary (arm64) circRNAprofiler_1.24.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/circRNAprofiler

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/circRNAprofiler

Bioc Package Browser https://code.bioconductor.org/browse/circRNAprofiler/

Package Short Url https://bioconductor.org/packages/circRNAprofiler/

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