Package: kissDE 1.27.0

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

kissDE_1.27.0.tar.gz
kissDE_1.27.0.zip(r-4.5)kissDE_1.27.0.zip(r-4.4)kissDE_1.27.0.zip(r-4.3)
kissDE_1.27.0.tgz(r-4.4-any)kissDE_1.27.0.tgz(r-4.3-any)
kissDE_1.27.0.tar.gz(r-4.5-noble)kissDE_1.27.0.tar.gz(r-4.4-noble)
kissDE_1.27.0.tgz(r-4.4-emscripten)kissDE_1.27.0.tgz(r-4.3-emscripten)
kissDE.pdf |kissDE.html✨
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-1.27.0(bioc 3.21)kissDE-1.25.0(bioc 3.20)

alternativesplicing differentialsplicing experimentaldesign genomicvariation rnaseq transcriptomics

6.16 score 3 stars 7 scripts 218 downloads 4 mentions 6 exports 189 dependencies

Last updated 23 days agofrom:f7cd1540a3. Checks:OK: 3 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 07 2024
R-4.5-win	WARNING	Nov 07 2024
R-4.5-linux	WARNING	Nov 07 2024
R-4.4-win	WARNING	Nov 07 2024
R-4.4-mac	OK	Nov 07 2024
R-4.3-win	WARNING	Nov 07 2024
R-4.3-mac	OK	Nov 07 2024

Exports:diffExpressedVariants exploreResults kissDE kissplice2counts qualityControl writeOutputKissDE

Dependencies:abind ade4 aods3 askpass assorthead backports base64enc beachmat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops boot broom BSgenome bslib bsseq cachem car carData caTools cli cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray DelayedMatrixStats dendextend Deriv DESeq2 digest doBy doParallel dplyr DSS DT ellipse emmeans estimability evaluate factoextra FactoMineR fansi farver fastmap flashClust fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gplots gridExtra gtable gtools HDF5Array highr htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcompView munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest permute pillar pixmap pkgconfig plyr polynom promises purrr quantreg R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools rstatix rtracklayer S4Arrays S4Vectors sass scales scatterplot3d shiny shinycssloaders snow sourcetools sp SparseArray SparseM sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

kissDE Reference Manual

Rendered fromkissDE.rnwusingutils::Sweaveon Nov 07 2024.

Last update: 2022-03-09
Started: 2016-02-02

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