Ularcirc
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Ularcirc.
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Bioconductor version: 3.9
Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.
Author: David Humphreys [aut, cre]
Maintainer: David Humphreys <d.humphreys at victorchang.edu.au>
citation("Ularcirc")
):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Ularcirc")
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("Ularcirc")
Ularcirc | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization |
Version | 1.2.21 |
In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
License | file LICENSE |
Depends | R (>= 3.4.0) |
Imports | AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, S4Vectors, shiny, shinyFiles, Sushi, yaml |
System Requirements | |
URL |
See More
Suggests | BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene |
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 | Ularcirc_1.2.21.tar.gz |
Windows Binary | Ularcirc_1.2.21.zip |
Mac OS X 10.11 (El Capitan) | Ularcirc_1.2.21.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/Ularcirc |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Ularcirc |
Bioc Package Browser | https://code.bioconductor.org/browse/Ularcirc/ |
Package Short Url | https://bioconductor.org/packages/Ularcirc/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.9 | Source Archive |