SpliceImpactR
An R package to identify functional impacts due to alternative RNA processing events
Bioconductor version: 3.24 · Package version: 1.1.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Works by taking in processed data from the HIT Index and/or rMATS and identifying how differentially used alternative RNA processing events lead to changes in protein function through various means. Primarily this is done through protein similarity, functional protein domain analysis, and domain-domain interaction changes. Notably, we both identify alterantive RNA processing event 'swaps' across condition and are able to perform holistic analyses regarding the impact of different RNA processing events.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpliceImpactR")Details
| Maintainer | Zachary Wakefield <zachpw@bu.edu> |
| Author | Zachary Wakefield [cre, aut] (ORCID: <https://orcid.org/0000-0002-9104-0934>), Ana Fiszbein [aut] |
| License | GPL-3 |
| Bug Reports | https://github.com/fiszbein-lab/SpliceImpactR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, AlternativeSplicing, DifferentialSplicing, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/SpliceImpactR/ |
Citation
From within R, enter citation("SpliceImpactR"):
Zachary Wakefield, Ana Fiszbein. SpliceImpactR: An R package to identify functional impacts due to alternative RNA processing events. doi:10.18129/B9.bioc.SpliceImpactR, R package version 1.1.0, https://bioconductor.org/packages/SpliceImpactR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpliceImpactR_1.1.0.tar.gz |
| macOS binary (arm64) | SpliceImpactR_1.1.0.tgz |
| macOS binary (x86_64) | SpliceImpactR_1.1.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: data.table, BiocFileCache, BiocParallel, Biostrings, GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db, dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer, scales, stats, tidyr, tools, utils, magrittr, methods, S4Vectors
Suggests: devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot, stringr, readr, tibble, BiocStyle, clusterProfiler, AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db