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circRNAprofiler

This is the development version of circRNAprofiler; for the stable release version, see circRNAprofiler.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL https://github.com/Aufiero/circRNAprofiler
Bug Reports https://github.com/Aufiero/circRNAprofiler/issues
See More
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_1.17.0.tar.gz
Windows Binary
macOS Binary (x86_64) circRNAprofiler_1.17.0.tgz
macOS Binary (arm64)
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