OutSplice
Comparison of Splicing Events between Tumor and Normal Samples
Bioconductor version: 3.23 · Package version: 1.12.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OutSplice")Details
| Maintainer | Theresa Guo <twguo@health.ucsd.edu> |
| Author | Joseph Bendik [aut] (ORCID: <https://orcid.org/0000-0003-0877-5639>), Sandhya Kalavacherla [aut] (ORCID: <https://orcid.org/0000-0003-0485-9042>), Michael Considine [aut] (ORCID: <https://orcid.org/0000-0002-8666-4857>), Bahman Afsari [aut] (ORCID: <https://orcid.org/0000-0001-8717-7199>), Michael F. Ochs [aut], Joseph Califano [aut] (ORCID: <https://orcid.org/0000-0002-4715-6761>), Daria A. Gaykalova [aut] (ORCID: <https://orcid.org/0000-0001-5037-0147>), Elana Fertig [aut] (ORCID: <https://orcid.org/0000-0003-3204-342X>), Theresa Guo [cre, aut] (ORCID: <https://orcid.org/0000-0002-1689-3275>) |
| License | GPL-2 |
| URL | https://github.com/GuoLabUCSD/OutSplice |
| Bug Reports | https://github.com/GuoLabUCSD/OutSplice/issues |
| Downloads rank | 403 |
| Source branch | RELEASE_3_23 |
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | OutSplice_1.12.0.tar.gz |
| Windows binary (x86_64) | OutSplice_1.12.0.zip |
| macOS binary (arm64) | OutSplice_1.12.0.tgz |
| macOS binary (x86_64) | OutSplice_1.12.0.tgz |