SpliceImpactR
This is the development version of SpliceImpactR; for the stable release version, see SpliceImpactR.
An R package to identify functional impacts due to alternative RNA processing events
Bioconductor version: Development (3.24)
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.
Author: Zachary Wakefield [cre, aut] 
, Ana Fiszbein [aut]
Maintainer: Zachary Wakefield <zachpw at bu.edu>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("SpliceImpactR")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("SpliceImpactR")| ORF-aware transcript-pair selection | HTML | |
| SpliceImpactR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, AlternativeSplicing, DifferentialSplicing, Software, StatisticalMethod |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | data.table, R.utils (>= 2.13.0), BiocFileCache, BiocParallel, Biostrings, GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db, dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer, scales, stats, tidyr, tools, utils, magrittr, methods, S4Vectors |
| System Requirements | |
| URL | https://github.com/fiszbein-lab/SpliceImpactR |
| Bug Reports | https://github.com/fiszbein-lab/SpliceImpactR/issues |
See More
| Suggests | devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot, stringr, readr, tibble, BiocStyle, clusterProfiler, AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpliceImpactR_1.1.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | SpliceImpactR_1.1.0.tgz |
| macOS Binary (sonoma-arm64) | SpliceImpactR_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpliceImpactR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpliceImpactR |
| Package Short Url | https://bioconductor.org/packages/SpliceImpactR/ |
| Package Downloads Report | Download Stats |