circRNAprofiler

DOI: 10.18129/B9.bioc.circRNAprofiler    

This is the development version of circRNAprofiler; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script circRNAprofiler
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction
Version 0.99.13
In Bioconductor since BioC 3.10 (R-3.6)
License GPL-3
Depends R (>= 3.6.0), gwascat
Imports dplyr, magrittr, readr, rtracklayer, stringr, Biostrings, BSgenome, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, AnnotationHub, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19
LinkingTo
Suggests testthat, knitr, roxygen2, rmarkdown, citr, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10
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_0.99.13.tar.gz
Windows Binary circRNAprofiler_0.99.13.zip
Mac OS X 10.11 (El Capitan) circRNAprofiler_0.99.13.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/
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