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circRNAprofiler

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License GPL-3
Depends R (>= 4.3.0)
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
Linking To
Suggests testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager
System Requirements
Enhances
URL https://github.com/Aufiero/circRNAprofiler
Bug Reports https://github.com/Aufiero/circRNAprofiler/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package circRNAprofiler_1.14.0.tar.gz
Windows Binary circRNAprofiler_1.14.0.zip
macOS Binary (x86_64) circRNAprofiler_1.14.0.tgz
macOS Binary (arm64) circRNAprofiler_1.14.0.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/
Package Downloads Report Download Stats