Prerequisites | Use case | Install and load kissDE | Quick start | kissDE's workflow | Input data | Condition vector | User's own data (without KisSplice): table of counts format | Input table from KisSplice output | Input table from KisSplice2refgenome output | Quality Control | Differential analysis | Output results | Final table | f/PSI table | kissDE's theory | Normalization | Estimation of dispersion | Pre-test filtering | Model fitting | Likelihood ratio test | Flagging low counts | Magnitude of the effect | Case studies | Application of kissDE to alternative splicing | Dataset | Load data | Quality control | Differential analysis | Export results | Explore results | One command to rule them all | Application of kissDE to SNPs/SNVs | Time / Requirements | Session info
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:
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)
alternativesplicingdifferentialsplicingexperimentaldesigngenomicvariationrnaseqtranscriptomicsquarto
Last updated from:2e4dd92d1a. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 237 | ||
| linux-devel-x86_64 | OK | 570 | ||
| source / vignettes | OK | 393 | ||
| linux-release-x86_64 | OK | 583 | ||
| macos-release-arm64 | OK | 291 | ||
| macos-oldrel-arm64 | OK | 300 | ||
| windows-devel | OK | 447 | ||
| windows-release | OK | 455 | ||
| windows-oldrel | OK | 425 | ||
| wasm-release | OK | 226 |
Exports:diffExpressedVariantsexploreResultskissDEkissplice2countsqualityControlwriteOutputKissDE
Dependencies:abindade4aods3askpassassortheadbackportsbase64encbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsbootbroomBSgenomebslibbsseqcachemcarcarDatacaToolscigarillocliclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdendextendDerivDESeq2digestdir.expirydoBydoParalleldplyrDSSDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapfilelockflashClustfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextgluegplotsgridExtragridtextgtablegtoolsh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalitedownlme4lmtestlocfitmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivopensslotelpbkrtestpermutepillarpixmappkgconfigpngpolynompromisespurrrquantregR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsrstatixrtracklayerS4ArraysS4VectorsS7sassscalesscatterplot3dSeqinfoshinyshinycssloadersshowtextshowtextdbsnowsourcetoolsspSparseArraySparseMsparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsyssysfontstibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzoo
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 |
