SPLINTER

This is the development version of SPLINTER; for the stable release version, see SPLINTER.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Splice Interpreter of Transcripts

Bioconductor version: Development (3.24)

Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.

Author: Diana Low [aut, cre]

Maintainer: Diana Low <lowdiana at gmail.com>

Citation (from within R, enter citation("SPLINTER")):

Diana Low. SPLINTER: Splice Interpreter of Transcripts. doi:10.18129/B9.bioc.SPLINTER, R package version 1.39.0, https://bioconductor.org/packages/SPLINTER.

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("SPLINTER")

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("SPLINTER")

SPLINTER	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, GeneExpression, ImmunoOncology, RNASeq, Software, Visualization
Version	1.39.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	GPL-2
Depends	R (>= 3.6.0), grDevices, stats
Imports	graphics, ggplot2, seqLogo, Biostrings, pwalign, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, Seqinfo, utils, plyr, stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis
System Requirements
URL	https://github.com/dianalow/SPLINTER/
Bug Reports	https://github.com/dianalow/SPLINTER/issues

Suggests	txdbmaker, BiocStyle, knitr, rmarkdown
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	SPLINTER_1.39.0.tar.gz
Windows Binary (x86_64)	SPLINTER_1.39.0.zip
macOS Binary (big-sur-x86_64)	SPLINTER_1.39.0.tgz
macOS Binary (sonoma-arm64)	SPLINTER_1.39.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPLINTER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SPLINTER
Package Short Url	https://bioconductor.org/packages/SPLINTER/
Package Downloads Report	Download Stats