SpliceWiz
This is the development version of SpliceWiz; for the stable release version, see SpliceWiz.
interactive analysis and visualization of alternative splicing in R
Bioconductor version: Development (3.22)
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb], William Ritchie [cph]
Maintainer: Alex Chit Hei Wong <alexchwong.github at gmail.com>
citation("SpliceWiz")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SpliceWiz")
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("SpliceWiz")| SpliceWiz: Quick Start | HTML | R Script |
| SpliceWiz: the cookbook | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GUI, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0), NxtIRFdata |
| Imports | ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, h5mread, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr |
| System Requirements | C++11, GNU make |
| URL | https://github.com/alexchwong/SpliceWiz |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread |
| Linking To | ompBAM, Rcpp, RcppProgress |
| 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 | SpliceWiz_1.11.0.tar.gz |
| Windows Binary (x86_64) | SpliceWiz_1.11.0.zip |
| macOS Binary (x86_64) | SpliceWiz_1.11.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpliceWiz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpliceWiz |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpliceWiz/ |
| Package Short Url | https://bioconductor.org/packages/SpliceWiz/ |
| Package Downloads Report | Download Stats |