{
  "_id": "6a49416f18cdde069385e056",
  "Package": "kissDE",
  "Version": "1.33.0",
  "Title": "Retrieves Condition-Specific Variants in RNA-Seq Data",
  "Description": "Retrieves condition-specific variants in RNA-seq data\n(SNVs, alternative-splicings, indels). It has been developed as\na post-treatment of 'KisSplice' but can also be used with\nuser's own data.",
  "Authors@R": "c(\nperson(\"Clara\", \"Benoit-Pilven\", email = \"clara.benoitp@gmail.com\", role = \"aut\"),\nperson(\"Camille\", \"Marchet\", email = \"camille.marchet@inria.fr\", role = \"aut\"),\nperson(\"Janice\", \"Kielbassa\", email = \"janice.kielbassa@lyon.unicancer.fr\", role = \"aut\"),\nperson(\"Lilia\", \"Brinza\", role = \"aut\"),\nperson(\"Audric\", \"Cologne\", email = \"audric.cologne@gmail.com\", role = \"aut\"),\nperson(\"Aurelie\", \"Siberchicot\", email = \"aurelie.siberchicot@univ-lyon1.fr\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7638-8318\")),\nperson(\"Vincent\", \"Lacroix\", email = \"vincent.lacroix@univ-lyon1.fr\", role = \"aut\"),\nperson(\"Frank\", \"Picard\", role = \"ctb\"),\nperson(\"Laurent\", \"Jacob\", role = \"ctb\"),\nperson(\"Vincent\", \"Miele\", role = \"ctb\"))",
  "License": "GPL (>= 2)",
  "Contact": "Vincent Lacroix <vincent.lacroix@univ-lyon1.fr>",
  "Encoding": "UTF-8",
  "biocViews": "AlternativeSplicing, DifferentialSplicing,\nExperimentalDesign, GenomicVariation, RNASeq, Transcriptomics",
  "URL": "https://github.com/lbbe-software/kissDE",
  "BugReports": "https://github.com/lbbe-software/kissDE/issues",
  "VignetteBuilder": "quarto",
  "Config/pak/sysreqs": "cmake libfreetype6-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:16 UTC",
  "RemoteUrl": "https://github.com/bioc/kissDE",
  "RemoteRef": "HEAD",
  "RemoteSha": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 08:06:54 UTC",
    "User": "root"
  },
  "Author": "Clara Benoit-Pilven [aut],\nCamille Marchet [aut],\nJanice Kielbassa [aut],\nLilia Brinza [aut],\nAudric Cologne [aut],\nAurelie Siberchicot [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7638-8318>),\nVincent Lacroix [aut],\nFrank Picard [ctb],\nLaurent Jacob [ctb],\nVincent Miele [ctb]",
  "Maintainer": "Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>",
  "_user": "bioc",
  "_type": "src",
  "_file": "kissDE_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/14ed2e7c6565a7e9ab89cae9c37acf83cd92aad38bad0651f2c5158d777244f6",
  "_filesize": 933086,
  "_sha256": "14ed2e7c6565a7e9ab89cae9c37acf83cd92aad38bad0651f2c5158d777244f6",
  "_expires": "2026-10-12T17:22:53.000Z",
  "_created": "2026-07-04T08:06:54.000Z",
  "_published": "2026-07-04T17:22:55.570Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488",
  "_status": "success",
  "_upstream": "https://github.com/bioc/kissDE",
  "_commit": {
    "id": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380436
  },
  "_maintainer": {
    "name": "Aurelie Siberchicot",
    "email": "aurelie.siberchicot@univ-lyon1.fr",
    "login": "aursiber",
    "description": "",
    "uuid": 13218953,
    "orcid": "0000-0002-7638-8318"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85151849214,
      "time": 237,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8079918240"
    },
    {
      "job": 85151849250,
      "time": 570,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079956930"
    },
    {
      "job": 85151849294,
      "time": 583,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079958217"
    },
    {
      "job": 85151849181,
      "time": 300,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8080223141"
    },
    {
      "job": 85151849171,
      "time": 291,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8080218153"
    },
    {
      "job": 85151849018,
      "time": 393,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079890228"
    },
    {
      "job": 85151849185,
      "time": 226,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8079916968"
    },
    {
      "job": 85151849213,
      "time": 447,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8079942479"
    },
    {
      "job": 85151849261,
      "time": 425,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8079940007"
    },
    {
      "job": 85151849216,
      "time": 455,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8079943455"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "aods3",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "DSS",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinycssloaders",
      "role": "Imports"
    },
    {
      "package": "ade4",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "quarto",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-13",
      "n": 8
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-15",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "alternativesplicing",
    "differentialsplicing",
    "experimentaldesign",
    "genomicvariation",
    "rnaseq",
    "transcriptomics",
    "quarto"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "aursiber",
      "count": 308,
      "uuid": 13218953
    },
    {
      "user": "audriccologne",
      "count": 201,
      "uuid": 244924252
    },
    {
      "user": "cbenoitp",
      "count": 164,
      "uuid": 35301937
    },
    {
      "user": "kamimrcht",
      "count": 129,
      "uuid": 8310244
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "pierregerenton",
      "count": 3,
      "uuid": 30559767
    },
    {
      "user": "vincent-lacroix",
      "count": 2,
      "uuid": 62440592
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/lbbe-software/kissde",
  "_searchresults": 8,
  "_quarto": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/kissDE.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/lbbe-software/kissde",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "diffExpressedVariants",
    "exploreResults",
    "kissDE",
    "kissplice2counts",
    "qualityControl",
    "writeOutputKissDE"
  ],
  "_help": [
    {
      "page": "kissDE-package",
      "title": "Retrieves condition-specific variants in RNA-seq data",
      "topics": [
        "kissDE-package"
      ]
    },
    {
      "page": "diffExpressedVariants",
      "title": "Retrieve condition-specific variants in RNA-seq data",
      "topics": [
        "diffExpressedVariants"
      ]
    },
    {
      "page": "exploreResults",
      "title": "Print kissDE results in an interactive Shiny application",
      "topics": [
        "exploreResults"
      ]
    },
    {
      "page": "kissDE",
      "title": "Run the whole kissDE analysis",
      "topics": [
        "kissDE"
      ]
    },
    {
      "page": "kissplice2counts",
      "title": "Conversion of 'KisSplice' or 'KisSplice2RefGenome' outputs",
      "topics": [
        "kissplice2counts"
      ]
    },
    {
      "page": "qualityControl",
      "title": "Quality control plots",
      "topics": [
        "qualityControl"
      ]
    },
    {
      "page": "writeOutputKissDE",
      "title": "Create and store the output of the 'diffExpressedVariants' function in a file and in a rds object.",
      "topics": [
        "writeOutputKissDE"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/kissDE/raw/HEAD/README.md",
  "_rundeps": [
    "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",
    "ggtext",
    "glue",
    "gplots",
    "gridExtra",
    "gridtext",
    "gtable",
    "gtools",
    "h5mread",
    "HDF5Array",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "limma",
    "litedown",
    "lme4",
    "lmtest",
    "locfit",
    "magrittr",
    "markdown",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "permute",
    "pillar",
    "pixmap",
    "pkgconfig",
    "png",
    "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",
    "showtext",
    "showtextdb",
    "snow",
    "sourcetools",
    "sp",
    "SparseArray",
    "SparseM",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "sysfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "urca",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "kissDE.qmd",
      "filename": "kissDE.html",
      "title": "kissDE Reference Manual",
      "engine": "quarto::html",
      "headings": [
        "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"
      ],
      "created": "2026-03-25 16:38:40",
      "modified": "2026-03-30 12:46:47",
      "commits": 3
    }
  ],
  "_score": 6.380211241711606,
  "_indexed": true,
  "_nocasepkg": "kissde",
  "_universes": [
    "bioc",
    "aursiber",
    "lbbe-software"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T08:11:55.000Z",
      "distro": "resolute",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/4400a8e0462b0f9469fc75cb8f1adc54b3ed7c186204683f2ab206f27fd6b7ab",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T08:12:08.000Z",
      "distro": "resolute",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/100514b5c8c2e2545cc98ab74517b7fb45d104695650d83c9e56a164a534c266",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T08:52:47.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/99f46988ae32c0c10f985a3bccf69b3345e3149bc76fbd7b303466ae75a776be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T08:52:09.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/a30edc1f585f2dea20f692125aa8b6afdc24d50c3f729f34003c6e61283cf16a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-07-04T08:11:30.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/fcfa00cf61659030ddf04c7101dcb7151d6c6b889f5d48eed789bd368bf80bc2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T08:09:30.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/7166c6a0710821b4979144b7babb75388dbc274e23a1352b235fb6a6efdf1060",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T08:09:37.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/4fcb5252e5260f97599b967db579f7bbb225ae8a66e7566b71568b6d514afb8f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T08:09:57.000Z",
      "commit": "2e4dd92d1a57606af7ccd4e4e16086959e2b05a1",
      "fileid": "https://r2.ropensci.org/e6f32b81d9bcaf578a7fbabb879cfcc52888a975d9a90be6bc0b3c8654a7ddf9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699889488"
    }
  ]
}