GeneStructureTools
This is the released version of GeneStructureTools; for the devel version, see GeneStructureTools.
Tools for spliced gene structure manipulation and analysis
Bioconductor version: Release (3.23)
GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.
Author: Beth Signal
Maintainer: Beth Signal <b.signal at garvan.org.au>
citation("GeneStructureTools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GeneStructureTools")
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("GeneStructureTools")| Introduction to GeneStructureTools | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialSplicing, FunctionalPrediction, ImmunoOncology, RNASeq, Software, Transcriptomics |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | |
| Imports | Biostrings, GenomicRanges, IRanges, data.table, plyr, stringdist, stringr, S4Vectors, BSgenome.Mmusculus.UCSC.mm10, stats, utils, Gviz, rtracklayer, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| 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 | GeneStructureTools_1.32.0.tar.gz |
| Windows Binary (x86_64) | GeneStructureTools_1.32.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | GeneStructureTools_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | GeneStructureTools_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GeneStructureTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GeneStructureTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/GeneStructureTools/ |
| Package Short Url | https://bioconductor.org/packages/GeneStructureTools/ |
| Package Downloads Report | Download Stats |