Package: kissDE 1.25.0
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_1.25.0.tar.gz
kissDE_1.25.0.zip(r-4.5)kissDE_1.25.0.zip(r-4.4)kissDE_1.25.0.zip(r-4.3)
kissDE_1.25.0.tgz(r-4.4-any)kissDE_1.25.0.tgz(r-4.3-any)
kissDE_1.25.0.tar.gz(r-4.5-noble)kissDE_1.25.0.tar.gz(r-4.4-noble)
kissDE_1.25.0.tgz(r-4.4-emscripten)kissDE_1.25.0.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-1.25.0(bioc 3.20)kissDE-1.24.0(bioc 3.19)
Last updated 2 months agofrom:a8b66599bc
Exports:diffExpressedVariantsexploreResultskissDEkissplice2countsqualityControlwriteOutputKissDE
Dependencies:abindade4aods3askpassbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomBSgenomebslibbsseqcachemcarcarDatacaToolscliclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdendextendDerivDESeq2digestdoBydoParalleldplyrDSSDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegplotsgridExtragtablegtoolsHDF5ArrayhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpermutepillarpixmappkgconfigplyrpolynompromisespurrrquantregR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsrstatixrtracklayerS4ArraysS4Vectorssassscalesscatterplot3dshinyshinycssloaderssnowsourcetoolsspSparseArraySparseMsparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc
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 |