{
  "_id": "6a1ad4771d7bb097a09e41ac",
  "Package": "DiffLogo",
  "Type": "Package",
  "Title": "DiffLogo: A comparative visualisation of biooligomer motifs",
  "Version": "2.37.0",
  "Date": "2015-02-12",
  "Author": "c( person(\"Martin\", \"Nettling\", role = c(\"aut\", \"cre\"), email =\n\"martin.nettling@informatik.uni-halle.de\"), person(\"Hendrik\",\n\"Treutler\", role = c(\"aut\", \"cre\"), email =\n\"hendrik.treutler@ipb-halle.de\"), person(\"Jan\", \"Grau\", role =\nc(\"aut\", \"ctb\"), email = \"grau@informatik.uni-halle.de\"),\nperson(\"Andrey\", \"Lando\", role = c(\"aut\", \"ctb\"), email =\n\"dronte@autosome.ru\"), person(\"Jens\", \"Keilwagen\", role =\nc(\"aut\", \"ctb\"), email = \"jens.keilwagen@julius-kuehn.de\"),\nperson(\"Stefan\", \"Posch\", role = \"aut\", email =\n\"posch@informatik.uni-halle.de\"), person(\"Ivo\", \"Grosse\", role\n= \"aut\", email = \"grosse@informatik.uni-halle.de\"))",
  "Maintainer": "Hendrik Treutler<hendrik.treutler@gmail.com>",
  "Description": "DiffLogo is an easy-to-use tool to visualize motif\ndifferences.",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/mgledi/DiffLogo/",
  "BugReports": "https://github.com/mgledi/DiffLogo/issues",
  "biocViews": "Software, SequenceMatching, MultipleComparison,\nMotifAnnotation, Visualization, Alignment",
  "Collate": "'alphabet.R' 'baseDistrs.R' 'diffSeqLogo.R' 'preconditions.R'\n'seqLogo.R' 'stackHeights.R' 'utilities.R'\n'diffSeqLogoSupport.R' 'pwmAlignment.R'",
  "RoxygenNote": "6.1.1",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:53 UTC",
  "RemoteUrl": "https://github.com/bioc/DiffLogo",
  "RemoteRef": "HEAD",
  "RemoteSha": "7b72497ee1b44a74738ba55f2ad483141a33049c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:43:06 UTC",
    "User": "root"
  },
  "MD5sum": "f3591fa19ee94d2061cd3c0dcf317695",
  "_user": "bioc",
  "_type": "src",
  "_file": "DiffLogo_2.37.0.tar.gz",
  "_fileid": "fa05a4b7ae18f1c812c1119358fdeeb814ca1b6b24562f015645a7a7ae4e8651",
  "_filesize": 1000196,
  "_sha256": "fa05a4b7ae18f1c812c1119358fdeeb814ca1b6b24562f015645a7a7ae4e8651",
  "_created": "2026-05-30T08:43:06.000Z",
  "_published": "2026-05-30T12:13:43.905Z",
  "_jobs": [
    {
      "job": 78637324301,
      "time": 151,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306927697"
    },
    {
      "job": 78637324307,
      "time": 162,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306928732"
    },
    {
      "job": 78637324305,
      "time": 162,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306928814"
    },
    {
      "job": 78637324304,
      "time": 121,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308082722"
    },
    {
      "job": 78637324330,
      "time": 135,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308084208"
    },
    {
      "job": 78637138267,
      "time": 209,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306913391"
    },
    {
      "job": 78637324296,
      "time": 122,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306924944"
    },
    {
      "job": 78637324340,
      "time": 108,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306923683"
    },
    {
      "job": 78637324325,
      "time": 104,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7306923303"
    },
    {
      "job": 78637324343,
      "time": 109,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306923721"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DiffLogo",
  "_commit": {
    "id": "7b72497ee1b44a74738ba55f2ad483141a33049c",
    "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": 1777380113
  },
  "_maintainer": {
    "name": "Hendrik Treutler",
    "email": "hendrik.treutler@gmail.com",
    "login": "treutler",
    "description": "Backend engineer at Tealium",
    "uuid": 7373384
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "cba",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "seqLogo",
      "role": "Suggests"
    },
    {
      "package": "MotifDb",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "sequencematching",
    "multiplecomparison",
    "motifannotation",
    "visualization",
    "alignment"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "dronte",
      "count": 35,
      "uuid": 3256572
    },
    {
      "user": "mgledi",
      "count": 33,
      "uuid": 4587006
    },
    {
      "user": "treutler",
      "count": 12,
      "uuid": 7373384
    },
    {
      "user": "fmaxbelemmi",
      "count": 2,
      "uuid": 26583296
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 404,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DiffLogo"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/mgledi/difflogo",
  "_searchresults": 48,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DiffLogo.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mgledi/difflogo",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Alphabet",
    "ASN",
    "calculatePvalue",
    "createDiffLogoObject",
    "differenceOfICs",
    "diffLogo",
    "diffLogoFromPwm",
    "diffLogoTable",
    "diffLogoTableConfiguration",
    "DNA",
    "drawDiffLogoTable",
    "enrichDiffLogoObjectWithPvalues",
    "enrichDiffLogoTableWithPvalues",
    "extendPwmsFromAlignmentVector",
    "FULL_ALPHABET",
    "getAlphabetFromCharacters",
    "getAlphabetFromSequences",
    "getPwmFromAlignment",
    "getPwmFromAlignmentFile",
    "getPwmFromFastaFile",
    "getPwmFromFile",
    "getPwmFromHomerFile",
    "getPwmFromPfmOrJasparFile",
    "getPwmFromPwmFile",
    "getSequencesFromAlignmentFile",
    "getSequencesFromFastaFile",
    "informationContent",
    "lossOfAbsICDifferences",
    "multipleLocalPwmsAlignment",
    "normalizedDifferenceOfProbabilities",
    "normalizePWM",
    "prepareDiffLogoTable",
    "probabilities",
    "pwmDivergence",
    "RNA",
    "seqLogo",
    "shannonDivergence",
    "sumOfAbsICDifferences",
    "sumOfAbsProbabilityDifferences",
    "sumProbabilities"
  ],
  "_help": [
    {
      "page": "alignPwmSets",
      "title": "Multiple PWMs alignment",
      "topics": [
        "alignPwmSets"
      ]
    },
    {
      "page": "Alphabet",
      "title": "built alphabet",
      "topics": [
        "Alphabet"
      ]
    },
    {
      "page": "ASN",
      "title": "ASN alphabet",
      "topics": [
        "ASN"
      ]
    },
    {
      "page": "baseDistributionPwm",
      "title": "Generates a PWM",
      "topics": [
        "baseDistributionPwm"
      ]
    },
    {
      "page": "calculatePvalue",
      "title": "p-value that two PWM-positions are from the same distribution",
      "topics": [
        "calculatePvalue"
      ]
    },
    {
      "page": "createDiffLogoObject",
      "title": "DiffLogo object",
      "topics": [
        "createDiffLogoObject"
      ]
    },
    {
      "page": "differenceOfICs",
      "title": "normalized information content differences",
      "topics": [
        "differenceOfICs"
      ]
    },
    {
      "page": "diffLogo",
      "title": "Draw DiffLogo",
      "topics": [
        "diffLogo"
      ]
    },
    {
      "page": "diffLogoFromPwm",
      "title": "Draw DiffLogo from PWM",
      "topics": [
        "diffLogoFromPwm"
      ]
    },
    {
      "page": "diffLogoTable",
      "title": "Draw DiffLogo-table",
      "topics": [
        "diffLogoTable"
      ]
    },
    {
      "page": "diffLogoTableConfiguration",
      "title": "Configuration object for diffLogoTable",
      "topics": [
        "diffLogoTableConfiguration"
      ]
    },
    {
      "page": "DNA",
      "title": "DNA alphabet",
      "topics": [
        "DNA"
      ]
    },
    {
      "page": "drawDiffLogoTable",
      "title": "Draws a table of DiffLogos",
      "topics": [
        "drawDiffLogoTable"
      ]
    },
    {
      "page": "enrichDiffLogoObjectWithPvalues",
      "title": "Enriches a difflogo object with p-values",
      "topics": [
        "enrichDiffLogoObjectWithPvalues"
      ]
    },
    {
      "page": "enrichDiffLogoTableWithPvalues",
      "title": "Enriches a matrix of difflogo objects with p-values",
      "topics": [
        "enrichDiffLogoTableWithPvalues"
      ]
    },
    {
      "page": "extendPwmsFromAlignmentVector",
      "title": "Extend pwms with respect to alignment",
      "topics": [
        "extendPwmsFromAlignmentVector"
      ]
    },
    {
      "page": "FULL_ALPHABET",
      "title": "Complete character alphabet",
      "topics": [
        "FULL_ALPHABET"
      ]
    },
    {
      "page": "getAlphabetFromCharacters",
      "title": "returns the alphabet which fits to the given characters",
      "topics": [
        "getAlphabetFromCharacters"
      ]
    },
    {
      "page": "getAlphabetFromSequences",
      "title": "returns the alphabet which fits to the given sequences",
      "topics": [
        "getAlphabetFromSequences"
      ]
    },
    {
      "page": "getPwmFromAlignment",
      "title": "Create PWM from alignment",
      "topics": [
        "getPwmFromAlignment"
      ]
    },
    {
      "page": "getPwmFromAlignmentFile",
      "title": "generates a pwm from an alignment file",
      "topics": [
        "getPwmFromAlignmentFile"
      ]
    },
    {
      "page": "getPwmFromFastaFile",
      "title": "generates a pwm from a FASTA file",
      "topics": [
        "getPwmFromFastaFile"
      ]
    },
    {
      "page": "getPwmFromFile",
      "title": "generates a pwm from a file of different formats",
      "topics": [
        "getPwmFromFile"
      ]
    },
    {
      "page": "getPwmFromHomerFile",
      "title": "generates a pwm from a homer file",
      "topics": [
        "getPwmFromHomerFile"
      ]
    },
    {
      "page": "getPwmFromPfmOrJasparFile",
      "title": "generates a pwm from a jaspar file",
      "topics": [
        "getPwmFromPfmOrJasparFile"
      ]
    },
    {
      "page": "getPwmFromPwmFile",
      "title": "generates a pwm from a pwm file",
      "topics": [
        "getPwmFromPwmFile"
      ]
    },
    {
      "page": "getSequencesFromAlignmentFile",
      "title": "extracts the sequences from an alignment file",
      "topics": [
        "getSequencesFromAlignmentFile"
      ]
    },
    {
      "page": "getSequencesFromFastaFile",
      "title": "extracts the sequences from a FASTA file",
      "topics": [
        "getSequencesFromFastaFile"
      ]
    },
    {
      "page": "informationContent",
      "title": "information content",
      "topics": [
        "informationContent"
      ]
    },
    {
      "page": "localPwmAlignment",
      "title": "Align pwms",
      "topics": [
        "localPwmAlignment"
      ]
    },
    {
      "page": "lossOfAbsICDifferences",
      "title": "the change of information content",
      "topics": [
        "lossOfAbsICDifferences"
      ]
    },
    {
      "page": "multipleLocalPwmsAlignment",
      "title": "Multiple PWMs alignment",
      "topics": [
        "multipleLocalPwmsAlignment"
      ]
    },
    {
      "page": "normalizedDifferenceOfProbabilities",
      "title": "normalized probability differences",
      "topics": [
        "normalizedDifferenceOfProbabilities"
      ]
    },
    {
      "page": "normalizePWM",
      "title": "normalizes the given pwm",
      "topics": [
        "normalizePWM"
      ]
    },
    {
      "page": "prepareDiffLogoTable",
      "title": "Prepare a table of difflogo objects",
      "topics": [
        "prepareDiffLogoTable"
      ]
    },
    {
      "page": "probabilities",
      "title": "probabilities",
      "topics": [
        "probabilities"
      ]
    },
    {
      "page": "pwmDivergence",
      "title": "PWM divergence",
      "topics": [
        "pwmDivergence"
      ]
    },
    {
      "page": "pwmsDistanceMatrix",
      "title": "Multiple PWMs alignment",
      "topics": [
        "pwmsDistanceMatrix"
      ]
    },
    {
      "page": "reverseAlignmentVector",
      "title": "Reverse for alignment vector",
      "topics": [
        "reverseAlignmentVector"
      ]
    },
    {
      "page": "RNA",
      "title": "RNA alphabet",
      "topics": [
        "RNA"
      ]
    },
    {
      "page": "seqLogo",
      "title": "Draw sequence logo",
      "topics": [
        "seqLogo"
      ]
    },
    {
      "page": "shannonDivergence",
      "title": "shannon divergence",
      "topics": [
        "shannonDivergence"
      ]
    },
    {
      "page": "sumOfAbsICDifferences",
      "title": "sum of absolute information content differences",
      "topics": [
        "sumOfAbsICDifferences"
      ]
    },
    {
      "page": "sumOfAbsProbabilityDifferences",
      "title": "sum of absolute probability differences",
      "topics": [
        "sumOfAbsProbabilityDifferences"
      ]
    },
    {
      "page": "sumProbabilities",
      "title": "sum of probabilities, i.e. 1.0",
      "topics": [
        "sumProbabilities"
      ]
    },
    {
      "page": "switchDirection",
      "title": "Switches between 'forward' and 'reverse'",
      "topics": [
        "switchDirection"
      ]
    },
    {
      "page": "twoSetsAveragePwmDivergenceFromAlignmentVector",
      "title": "Average divergence between two sets.",
      "topics": [
        "twoSetsAveragePwmDivergenceFromAlignmentVector"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DiffLogo/raw/HEAD/README.md",
  "_rundeps": [
    "cba",
    "proxy"
  ],
  "_vignettes": [
    {
      "source": "DiffLogoBasics.Rnw",
      "filename": "DiffLogoBasics.pdf",
      "title": "Basics of the DiffLogo package",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2015-09-28 14:38:37",
      "modified": "2017-07-07 10:46:55",
      "commits": 2
    }
  ],
  "_score": 6.90655051910145,
  "_indexed": true,
  "_nocasepkg": "difflogo",
  "_universes": [
    "bioc",
    "treutler",
    "mgledi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.37.0",
      "date": "2026-05-30T08:45:46.000Z",
      "distro": "noble",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "b7fad77d7259dd2ae497e4876bdc8a6469886585263f65e23170bb7df42345bc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.37.0",
      "date": "2026-05-30T08:45:48.000Z",
      "distro": "noble",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "7c9248d0b8b459683ea6c1f425c9d1769d412696b6195e6705a25917ad63d46d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.37.0",
      "date": "2026-05-30T12:12:52.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "6137dee10ed73594930bdda09651854149b73afde1b3f14bdc7daa207bccc446",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.37.0",
      "date": "2026-05-30T12:13:14.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "aeabba15427e88e82fd50d206926b9b5a200402cd8dfc4f7ff378ff3cd3bd7d7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.37.0",
      "date": "2026-05-30T08:45:24.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "b13d98280eccd201d25fda6bed5d8ed8b7123990323ac409ff69417d244cd2cc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.37.0",
      "date": "2026-05-30T08:44:44.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "5803ae1d72d3ceb387d46d1fc2c0cffb97ecd3214cb389778e7cf84124867c5b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.37.0",
      "date": "2026-05-30T08:44:41.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "3d17ec91ae07ceb2b865dcf02817a8737ed7377ae7aad276e710188089047c24",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.37.0",
      "date": "2026-05-30T08:44:49.000Z",
      "commit": "7b72497ee1b44a74738ba55f2ad483141a33049c",
      "fileid": "996747031490d2426cb9f580b9ceeb9d27a930dea931f15a58aeb1571fc6c0ac",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679452605"
    }
  ]
}