OutSplice
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see OutSplice.
Comparison of Splicing Events between Tumor and Normal Samples
Bioconductor version: 3.19
An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.
Author: Joseph Bendik [aut] 
, Sandhya Kalavacherla [aut] , Michael Considine [aut] , Bahman Afsari [aut] , Michael F. Ochs [aut], Joseph Califano [aut] , Daria A. Gaykalova [aut] , Elana Fertig [aut] , Theresa Guo [cre, aut]
Maintainer: Theresa Guo <twguo at health.ucsd.edu>
citation("OutSplice")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OutSplice")
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("OutSplice")| Find Splicing Outliers in Tumor Samples with OutSplice | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.3) |
| Imports | AnnotationDbi(>= 1.60.0), GenomicRanges(>= 1.49.0), GenomicFeatures(>= 1.50.2), IRanges(>= 2.32.0), org.Hs.eg.db(>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene(>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene(>= 3.16.0), S4Vectors(>= 0.36.0) |
| System Requirements | |
| URL | https://github.com/GuoLabUCSD/OutSplice |
| Bug Reports | https://github.com/GuoLabUCSD/OutSplice/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| 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 | OutSplice_1.4.0.tar.gz |
| Windows Binary (x86_64) | OutSplice_1.4.0.zip |
| macOS Binary (x86_64) | OutSplice_1.4.0.tgz |
| macOS Binary (arm64) | OutSplice_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/OutSplice |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OutSplice |
| Bioc Package Browser | https://code.bioconductor.org/browse/OutSplice/ |
| Package Short Url | https://bioconductor.org/packages/OutSplice/ |
| Package Downloads Report | Download Stats |