circRNAprofiler

DOI: 10.18129/B9.bioc.circRNAprofiler    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see circRNAprofiler.

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

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	circRNAprofiler
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction
Version	1.4.2
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
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
LinkingTo
Suggests	testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager
SystemRequirements
Enhances
URL	https://github.com/Aufiero/circRNAprofiler
BugReports	https://github.com/Aufiero/circRNAprofiler/issues
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_1.4.2.tar.gz
Windows Binary	circRNAprofiler_1.4.2.zip
macOS 10.13 (High Sierra)	circRNAprofiler_1.4.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/circRNAprofiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/circRNAprofiler
Package Short Url	https://bioconductor.org/packages/circRNAprofiler/
Package Downloads Report	Download Stats