casper
This is the development version of casper; for the stable release version, see casper.
Characterization of Alternative Splicing Based on Paired-End Reads
Bioconductor version: Development (3.24)
Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Author: David Rossell [aut, cre], Camille Stephan-Otto [aut], Manuel Kroiss [aut], Miranda Stobbe [aut], Victor Pena [aut]
Maintainer: David Rossell <rosselldavid at gmail.com>
citation("casper")):
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("casper")
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("casper")| DesignRNASeq.pdf | ||
| Manual for the casper library | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
| Version | 2.47.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges |
| Imports | BiocGenerics(>= 0.31.6), coda, EBarrays, gaga, gtools, Seqinfo, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors(>= 0.9.25), sqldf, survival, txdbmaker, VGAM |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | parallel |
| 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 | casper_2.47.0.tar.gz |
| Windows Binary (x86_64) | casper_2.47.0.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/casper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/casper |
| Bioc Package Browser | https://code.bioconductor.org/browse/casper/ |
| Package Short Url | https://bioconductor.org/packages/casper/ |
| Package Downloads Report | Download Stats |