SplicingGraphs
This is the development version of SplicingGraphs; for the stable release version, see SplicingGraphs.
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Bioconductor version: Development (3.24)
This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès
Maintainer: H. Pagès <hpages.on.github at gmail.com>
citation("SplicingGraphs")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("SplicingGraphs")
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("SplicingGraphs")| Splicing graphs and RNA-seq data | R Script | |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7) |
| Imports | methods, utils, graphics, igraph, BiocGenerics, S4Vectors(>= 0.17.5), BiocParallel, IRanges(>= 2.21.2), Seqinfo, GenomicRanges(>= 1.23.21), Rsamtools, graph |
| System Requirements | |
| URL | https://bioconductor.org/packages/SplicingGraphs |
| Bug Reports | https://github.com/Bioconductor/SplicingGraphs/issues |
See More
| Suggests | igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.refGene, RNAseqData.HNRNPC.bam.chr14, RUnit |
| 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 | SplicingGraphs_1.53.0.tar.gz |
| Windows Binary (x86_64) | SplicingGraphs_1.53.0.zip |
| macOS Binary (big-sur-x86_64) | SplicingGraphs_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | SplicingGraphs_1.53.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SplicingGraphs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SplicingGraphs |
| Bioc Package Browser | https://code.bioconductor.org/browse/SplicingGraphs/ |
| Package Short Url | https://bioconductor.org/packages/SplicingGraphs/ |
| Package Downloads Report | Download Stats |