kissDE

This is the released version of kissDE; for the devel version, see kissDE.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

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] ORCID: 0000-0002-7638-8318 , Vincent Lacroix [aut], Frank Picard [ctb], Laurent Jacob [ctb], Vincent Miele [ctb]

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

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

Clara Benoit-Pilven, Camille Marchet, Janice Kielbassa, Lilia Brinza, Audric Cologne, Aurelie Siberchicot, Vincent Lacroix. kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data. doi:10.18129/B9.bioc.kissDE, R package version 1.32.0, https://bioconductor.org/packages/kissDE.

Generated from the package metadata; it may differ from the package's own citation.

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	PDF

Need some help? Ask on the Bioconductor Support site!

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

Suggests	BiocStyle, quarto, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

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
Package Short Url	https://bioconductor.org/packages/kissDE/
Package Downloads Report	Download Stats