circRNAprofiler
This is the released version of circRNAprofiler; for the devel version, see circRNAprofiler.
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
Bioconductor version: Release (3.23)
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("circRNAprofiler")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, DifferentialExpression, FunctionalPrediction, GenePrediction, GenomeAssembly, Software, StructuralPrediction |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | circRNAprofiler_1.26.0.tar.gz |
| Windows Binary (x86_64) | circRNAprofiler_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | circRNAprofiler_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | circRNAprofiler_1.26.0.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 |