This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see circRNAprofiler.
Bioconductor version: 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")
):
To install this package, start R (version "3.6") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("circRNAprofiler")
HTML | R Script | circRNAprofiler |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction |
Version | 1.0.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (< 6 months) |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | circRNAprofiler_1.0.0.tar.gz |
Windows Binary | circRNAprofiler_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | circRNAprofiler_1.0.0.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 |
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