Ularcirc
This package is for version 3.11 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: 3.11
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 "4.0") 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 | 1.6.0 |
| 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, moments, Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, 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_1.6.0.tar.gz |
| Windows Binary | Ularcirc_1.6.0.zip |
| macOS 10.13 (High Sierra) | Ularcirc_1.6.0.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 3.11 | Source Archive |