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kissDE

Retrieves Condition-Specific Variants in RNA-Seq Data


Bioconductor version: Release (3.18)

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], Aurélie Siberchicot [aut, cre], Vincent Lacroix [aut], Frank Picard [ctb], Laurent Jacob [ctb], Vincent Miele [ctb]

Maintainer: Aurélie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>

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

Installation

To install this package, start R (version "4.3") 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.pdf PDF R Script
Reference Manual PDF

Details

biocViews AlternativeSplicing, DifferentialSplicing, ExperimentalDesign, GenomicVariation, RNASeq, Software, Transcriptomics
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package kissDE_1.22.0.tar.gz
Windows Binary kissDE_1.22.0.zip (64-bit only)
macOS Binary (x86_64) kissDE_1.22.0.tgz
macOS Binary (arm64) kissDE_1.22.0.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