Package: kissDE 1.33.0

Aurelie Siberchicot

kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

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.

Authors: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]

kissDE_1.33.0.tar.gz
kissDE_1.33.0.zip(r-4.7)kissDE_1.33.0.zip(r-4.6)kissDE_1.33.0.zip(r-4.5)
kissDE_1.33.0.tgz(r-4.6-any)kissDE_1.33.0.tgz(r-4.5-any)
kissDE_1.33.0.tar.gz(r-4.7-any)kissDE_1.33.0.tar.gz(r-4.6-any)
kissDE_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
kissDE/json (API)

# Install 'kissDE' in R:

install.packages('kissDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lbbe-software/kissde/issues

On BioConductor:kissDE-1.33.0(bioc 3.24)kissDE-1.32.0(bioc 3.23)

alternativesplicing differentialsplicing experimentaldesign genomicvariation rnaseq transcriptomics quarto

6.38 score 3 stars 7 scripts 360 downloads 4 mentions 6 exports 199 dependencies

Last updated from:2e4dd92d1a. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	267
linux-devel-x86_64	OK	517
source / vignettes	OK	399
linux-release-x86_64	OK	547
macos-release-arm64	OK	399
macos-oldrel-arm64	OK	288
windows-devel	OK	431
windows-release	OK	481
windows-oldrel	OK	423
wasm-release	OK	194

Exports:diffExpressedVariants exploreResults kissDE kissplice2counts qualityControl writeOutputKissDE

Dependencies:abind ade4 aods3 askpass assorthead backports base64enc beachmat BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops boot broom BSgenome bslib bsseq cachem car carData caTools cigarillo cli cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray DelayedMatrixStats dendextend Deriv DESeq2 digest dir.expiry doBy doParallel dplyr DSS DT ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap filelock flashClust fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gplots gridExtra gtable gtools h5mread HDF5Array highr htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv openssl otel pbkrtest permute pillar pixmap pkgconfig polynom promises purrr quantreg R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools rstatix rtracklayer S4Arrays S4Vectors S7 sass scales scatterplot3d Seqinfo shiny shinycssloaders snow sourcetools sp SparseArray SparseM sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zoo

kissDE Reference Manual

Rendered fromkissDE.qmdusingquarto::html

Last update: 2026-03-30
Started: 2026-03-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieves condition-specific variants in RNA-seq data	kissDE-package
Retrieve condition-specific variants in RNA-seq data	diffExpressedVariants
Print kissDE results in an interactive Shiny application	exploreResults
Run the whole kissDE analysis	kissDE
Conversion of 'KisSplice' or 'KisSplice2RefGenome' outputs	kissplice2counts
Quality control plots	qualityControl
Create and store the output of the 'diffExpressedVariants' function in a file and in a rds object.	writeOutputKissDE