kissDE
This is the released version of kissDE; for the devel version, see kissDE.
Retrieves Condition-Specific Variants in RNA-Seq Data
Bioconductor version: Release (3.23)
Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.
Author: Clara Benoit-Pilven [aut], Camille Marchet [aut], Janice Kielbassa [aut], Lilia Brinza [aut], Audric Cologne [aut], Aurelie Siberchicot [aut, cre]
, Vincent Lacroix [aut], Frank Picard [ctb], Laurent Jacob [ctb], Vincent Miele [ctb]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>
citation("kissDE")):
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("kissDE")
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("kissDE")| kissDE.html | HTML | R Script |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, DifferentialSplicing, ExperimentalDesign, GenomicVariation, RNASeq, Software, Transcriptomics |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL (>= 2) |
| Depends | |
| Imports | aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel, shiny, shinycssloaders, ade4, factoextra, DT, rlang |
| System Requirements | |
| URL | https://github.com/lbbe-software/kissDE |
| Bug Reports | https://github.com/lbbe-software/kissDE/issues |
See More
| Suggests | BiocStyle, quarto, testthat |
| 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 | kissDE_1.32.0.tar.gz |
| Windows Binary (x86_64) | kissDE_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | kissDE_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | kissDE_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/kissDE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/kissDE |
| Bioc Package Browser | https://code.bioconductor.org/browse/kissDE/ |
| Package Short Url | https://bioconductor.org/packages/kissDE/ |
| Package Downloads Report | Download Stats |