{ "_id": "6a196991acfb0bcc41de942d", "Package": "CDI", "Version": "1.11.0", "Date": "2026-03-15", "Title": "Clustering Deviation Index (CDI)", "Description": "Single-cell RNA-sequencing (scRNA-seq) is widely used to\nexplore cellular variation. The analysis of scRNA-seq data\noften starts from clustering cells into subpopulations. This\ninitial step has a high impact on downstream analyses, and\nhence it is important to be accurate. However, there have not\nbeen unsupervised metric designed for scRNA-seq to evaluate\nclustering performance. Hence, we propose clustering deviation\nindex (CDI), an unsupervised metric based on the modeling of\nscRNA-seq UMI counts to evaluate clustering of cells.", "Authors@R": "c(person(\"Jiyuan\", \"Fang\", email = \"jfanglovestats@gmail.com\", role = c(\"cre\", \"aut\"), comment=c(ORCID=\"0000-0002-5004-4138\")), \nperson(\"Jichun\", \"Xie\", email = \"jichun.xie@duke.edu\", role = c(\"ctb\")),\nperson(\"Cliburn\", \"Chan\", email = \"cliburn.chan@duke.edu\", role = c(\"ctb\")),\nperson(\"Kouros\", \"Owzar\", email = \"kouros.owzar@duke.edu\", role = c(\"ctb\")),\nperson(\"Liuyang\", \"Wang\", email = \"liuyang.wang@duke.edu\", role = c(\"ctb\")),\nperson(\"Diyuan\", \"Qin\", email = \"diyuan.qin@duke.edu\", role = c(\"ctb\")),\nperson(\"Qi-Jing\", \"Li\", email = \"qi-jing.li@duke.edu\", role = c(\"ctb\")))", "biocViews": "SingleCell, Software, Clustering, Visualization, Sequencing,\nRNASeq, CellBasedAssays", "URL": "https://github.com/jichunxie/CDI", "BugReports": "https://github.com/jichunxie/CDI/issues", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:09 UTC", "RemoteUrl": "https://github.com/bioc/CDI", "RemoteRef": "HEAD", "RemoteSha": "191ae443191765e67e31d38ed1a0da1df314157c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:33:57 UTC", "User": "root" }, "Author": "Jiyuan Fang [cre, aut] (ORCID: ),\nJichun Xie [ctb],\nCliburn Chan [ctb],\nKouros Owzar [ctb],\nLiuyang Wang [ctb],\nDiyuan Qin [ctb],\nQi-Jing Li [ctb]", "Maintainer": "Jiyuan Fang ", "MD5sum": "93f747c509528d9cab4e5bbb1927cb51", "_user": "bioc", "_type": "src", "_file": "CDI_1.11.0.tar.gz", "_fileid": "06391962f4d8d26a37032b0e483f8e4373b65cac2ca9566f9d145e382536c321", "_filesize": 1990549, "_sha256": "06391962f4d8d26a37032b0e483f8e4373b65cac2ca9566f9d145e382536c321", "_created": "2026-05-29T08:33:57.000Z", "_published": "2026-05-29T10:25:21.623Z", "_jobs": [ { "job": 78466499564, "time": 233, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7286608195" }, { "job": 78466499524, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286678355" }, { "job": 78466499547, "time": 371, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286646994" }, { "job": 78466499602, "time": 356, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7288488961" }, { "job": 78466499587, "time": 202, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7288462359" }, { "job": 78465010700, "time": 610, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286538681" }, { "job": 78466499505, "time": 177, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": 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"b1_rc380", "b1_rc381", "b1_rc382", "b1_rc383", "b1_rc384", "b1_rc385", "b1_rc386", "b1_rc387", "b1_rc388", "b1_rc389", "b1_rc390", "b1_rc391", "b1_rc392", "b1_rc393", "b1_rc394", "b1_rc395", "b1_rc396", "b1_rc397", "b1_rc398", "b1_rc399", "b1_rc400", "b1_rc401", "b1_rc402", "b1_rc403", "b1_rc404", "b1_rc405", "b1_rc406", "b1_rc407", "b1_rc408", "b1_rc409", "b1_rc410", "b1_rc411", "b1_rc412", "b1_rc413", "b1_rc414", "b1_rc415", "b1_rc416", "b1_rc417", "b1_rc418", "b1_rc419", "b1_rc420", "b1_rc421", "b1_rc422", "b1_rc423", "b1_rc424", "b1_rc425", "b1_rc426", "b1_rc427", "b1_rc428", "b1_rc429", "b1_rc430", "b1_rc431", "b1_rc432", "b1_rc433", "b1_rc434", "b1_rc435", "b1_rc436", "b1_rc437", "b1_rc438", "b1_rc439", "b1_rc440", "b1_rc441", "b1_rc442", "b1_rc443", "b1_rc444", "b1_rc445", "b1_rc446", "b1_rc447", "b1_rc448", "b1_rc449", "b1_rc450", "b1_rc451", "b1_rc452", "b1_rc453", "b1_rc454", "b1_rc455", "b1_rc456", "b1_rc457", "b1_rc458", "b1_rc459", "b1_rc460", "b1_rc461", "b1_rc462", "b1_rc463", "b1_rc464", "b1_rc465", "b1_rc466", "b1_rc467", "b1_rc468", "b1_rc469", "b1_rc470", "b1_rc471", "b1_rc472", "b1_rc473", "b1_rc474", "b1_rc475", "b1_rc476", "b1_rc477", "b1_rc478", "b1_rc479", "b1_rc480", "b1_rc481", "b1_rc482", "b1_rc483", "b1_rc484", "b1_rc485", "b1_rc486", "b1_rc487", "b1_rc488", "b1_rc489", "b1_rc490", "b1_rc491", "b1_rc492", "b1_rc493", "b1_rc494", "b1_rc495", "b1_rc496", "b1_rc497", "b1_rc498", "b1_rc499", "b1_rc500", "b1_rc501", "b1_rc502", "b1_rc503", "b1_rc504", "b1_rc505", "b1_rc506", "b1_rc507", "b1_rc508", "b1_rc509", "b1_rc510", "b1_rc511", "b1_rc512", "b1_rc513", "b1_rc514", "b1_rc515", "b1_rc516", "b1_rc517", "b1_rc518", "b1_rc519", "b1_rc520", "b1_rc521", "b1_rc522", "b1_rc523", "b1_rc524", "b1_rc525", "b1_rc526", "b1_rc527", "b1_rc528", "b1_rc529", "b1_rc530", "b1_rc531", "b1_rc532", "b1_rc533", "b1_rc534", "b1_rc535", "b1_rc536", "b1_rc537", "b1_rc538", "b1_rc539", "b1_rc540", "b1_rc541", "b1_rc542", "b1_rc543", "b1_rc544", "b1_rc545", "b1_rc546", "b1_rc547", "b1_rc548", "b1_rc549", "b1_rc550", "b1_rc551", "b1_rc552", "b1_rc553", "b1_rc554", "b1_rc555", "b1_rc556", "b1_rc557", "b1_rc558", "b1_rc559", "b1_rc560", "b1_rc561", "b1_rc562", "b1_rc563", "b1_rc564", "b1_rc565", "b1_rc566", "b1_rc567", "b1_rc568", "b1_rc569", "b1_rc570", "b1_rc571", "b1_rc572", "b1_rc573", "b1_rc574", "b1_rc575", "b1_rc576", "b1_rc577", "b1_rc578", "b1_rc579", "b1_rc580", "b1_rc581", "b1_rc582", "b1_rc583", "b1_rc584", "b1_rc585", "b1_rc586", "b1_rc587", "b1_rc588", "b1_rc589", "b1_rc590", "b1_rc591", "b1_rc592", "b1_rc593", "b1_rc594", "b1_rc595", "b1_rc596", "b1_rc597", "b1_rc598", "b1_rc599", "b1_rc600", "b1_rc601", "b1_rc602", "b1_rc603", "b1_rc604", "b1_rc605", "b1_rc606", "b1_rc607", "b1_rc608", "b1_rc609", "b1_rc610", "b1_rc611", "b1_rc612", "b1_rc613", "b1_rc614", "b1_rc615", "b1_rc616", "b1_rc617", "b1_rc618", "b1_rc619", "b1_rc620", "b1_rc621", "b1_rc622", "b1_rc623", "b1_rc624", "b1_rc625", "b1_rc626", "b1_rc627", "b1_rc628", "b1_rc629", "b1_rc630", "b1_rc631", "b1_rc632", "b1_rc633", "b1_rc634", "b1_rc635", "b1_rc636", "b1_rc637", "b1_rc638", "b1_rc639", "b1_rc640", "b1_rc641", "b1_rc642", "b1_rc643", "b1_rc644", "b1_rc645", "b1_rc646", "b1_rc647", "b1_rc648", "b1_rc649", "b1_rc650", "b1_rc651", "b1_rc652", "b1_rc653", "b1_rc654", "b1_rc655", "b1_rc656", "b1_rc657", "b1_rc658", "b1_rc659", "b1_rc660", "b1_rc661", "b1_rc662", "b1_rc663", "b1_rc664", "b1_rc665", "b1_rc666", "b1_rc667", "b1_rc668", "b1_rc669", "b1_rc670", "b1_rc671", "b1_rc672", "b1_rc673", "b1_rc674", "b1_rc675", "b1_rc676", "b1_rc677", "b1_rc678", "b1_rc679", "b1_rc680", "b1_rc681", "b1_rc682", "b1_rc683", "b1_rc684", "b1_rc685", "b1_rc686", "b1_rc687", "b1_rc688", "b1_rc689", "b1_rc690", "b1_rc691", "b1_rc692", "b1_rc693", "b1_rc694", "b1_rc695", "b1_rc696", "b1_rc697", "b1_rc698", "b1_rc699", "b1_rc700", "b1_rc701", "b1_rc702", "b1_rc703", "b1_rc704", "b1_rc705", "b1_rc706", "b1_rc707", "b1_rc708", "b1_rc709", "b1_rc710", "b1_rc711", "b1_rc712", "b1_rc713", "b1_rc714", "b1_rc715", "b1_rc716", "b1_rc717", "b1_rc718", "b1_rc719", "b1_rc720", "b1_rc721", "b1_rc722", "b1_rc723", "b1_rc724", "b1_rc725", "b1_rc726", "b1_rc727", "b1_rc728", "b1_rc729", "b1_rc730", "b1_rc731", "b1_rc732", "b1_rc733", "b1_rc734", "b1_rc735", "b1_rc736", "b1_rc737", "b1_rc738", "b1_rc739", "b1_rc740", "b1_rc741", "b1_rc742", "b1_rc743", "b1_rc744", "b1_rc745", "b1_rc746", "b1_rc747", "b1_rc748", "b1_rc749", "b1_rc750", "b1_rc751", "b1_rc752", "b1_rc753", "b1_rc754", "b1_rc755", "b1_rc756", "b1_rc757", "b1_rc758", "b1_rc759", "b1_rc760", "b1_rc761", "b1_rc762", "b1_rc763", "b1_rc764", "b1_rc765", "b1_rc766", "b1_rc767", "b1_rc768", "b1_rc769", "b1_rc770", "b1_rc771", "b1_rc772", "b1_rc773", "b1_rc774", "b1_rc775", "b1_rc776", "b1_rc777", "b1_rc778", "b1_rc779", "b1_rc780", "b1_rc781", "b1_rc782", "b1_rc783", "b1_rc784", "b1_rc785", "b1_rc786", "b1_rc787", "b1_rc788", "b1_rc789", "b1_rc790", "b1_rc791", "b1_rc792", "b1_rc793", "b1_rc794", "b1_rc795", "b1_rc796", "b1_rc797", "b1_rc798", "b1_rc799", "b1_rc800", "b1_rc801", "b1_rc802", "b1_rc803", "b1_rc804", "b1_rc805", "b1_rc806", "b1_rc807", "b1_rc808", "b1_rc809", "b1_rc810", "b1_rc811", "b1_rc812", "b1_rc813", "b1_rc814", "b1_rc815", "b1_rc816", "b1_rc817", "b1_rc818", "b1_rc819", "b1_rc820", "b1_rc821", "b1_rc822", "b1_rc823", "b1_rc824", "b1_rc825", "b1_rc826", "b1_rc827", "b1_rc828", "b1_rc829", "b1_rc830", "b1_rc831", "b1_rc832", "b1_rc833", "b1_rc834", "b1_rc835", "b1_rc836", "b1_rc837", "b1_rc838", "b1_rc839", "b1_rc840", "b1_rc841", "b1_rc842", "b1_rc843", "b1_rc844", "b1_rc845", "b1_rc846", "b1_rc847", "b1_rc848", "b1_rc849", "b1_rc850", "b1_rc851", "b1_rc852", "b1_rc853", "b1_rc854", "b1_rc855", "b1_rc856", "b1_rc857", "b1_rc858", "b1_rc859", "b1_rc860", "b1_rc861", "b1_rc862", "b1_rc863", "b1_rc864", "b1_rc865", "b1_rc866", "b1_rc867", "b1_rc868", "b1_rc869", "b1_rc870", "b1_rc871", "b1_rc872", "b1_rc873", "b1_rc874", "b1_rc875", "b1_rc876", "b1_rc877", "b1_rc878", "b1_rc879", "b1_rc880", "b1_rc881", "b1_rc882", "b1_rc883", "b1_rc884", "b1_rc885", "b1_rc886", "b1_rc887", "b1_rc888", "b1_rc889", "b1_rc890", "b1_rc891", "b1_rc892", "b1_rc893", "b1_rc894", "b1_rc895", "b1_rc896", "b1_rc897", "b1_rc898", "b1_rc899", "b1_rc900", "b1_rc901", "b1_rc902", "b1_rc903", "b1_rc904", "b1_rc905", "b1_rc906", "b1_rc907", "b1_rc908", "b1_rc909", "b1_rc910", "b1_rc911", "b1_rc912", "b1_rc913", "b1_rc914", "b1_rc915", "b1_rc916", "b1_rc917", "b1_rc918", "b1_rc919", "b1_rc920", "b1_rc921", "b1_rc922", "b1_rc923", "b1_rc924", "b1_rc925", "b1_rc926", "b1_rc927", "b1_rc928", "b1_rc929", "b1_rc930", "b1_rc931", "b1_rc932", "b1_rc933", "b1_rc934", "b1_rc935", "b1_rc936", "b1_rc937", "b1_rc938", "b1_rc939", "b1_rc940", "b1_rc941", "b1_rc942", "b1_rc943", "b1_rc944", "b1_rc945", "b1_rc946", "b1_rc947", "b1_rc948", "b1_rc949", "b1_rc950", "b1_rc951", "b1_rc952", "b1_rc953", "b1_rc954", "b1_rc955", "b1_rc956", "b1_rc957", "b1_rc958", "b1_rc959", "b1_rc960", "b1_rc961", "b1_rc962", "b1_rc963", "b1_rc964", "b1_rc965", "b1_rc966", "b1_rc967", "b1_rc968", "b1_rc969", "b1_rc970", "b1_rc971", "b1_rc972", "b1_rc973", "b1_rc974", "b1_rc975", "b1_rc976", "b1_rc977", "b1_rc978", "b1_rc979", "b1_rc980", "b1_rc981", "b1_rc982", "b1_rc983", "b1_rc984", "b1_rc985", "b1_rc986", "b1_rc987", "b1_rc988", "b1_rc989", "b1_rc990", "b1_rc991", "b1_rc992", "b1_rc993", "b1_rc994", "b1_rc995", "b1_rc996", "b1_rc997", "b1_rc998", "b1_rc999", "b1_rc1000", "b2_rc1", "b2_rc2", "b2_rc3", "b2_rc4", "b2_rc5", "b2_rc6", "b2_rc7", "b2_rc8", "b2_rc9", "b2_rc10", "b2_rc11", "b2_rc12", "b2_rc13", "b2_rc14", "b2_rc15", "b2_rc16", "b2_rc17", "b2_rc18", "b2_rc19", "b2_rc20", "b2_rc21", "b2_rc22", "b2_rc23", "b2_rc24", "b2_rc25", "b2_rc26", "b2_rc27", "b2_rc28", "b2_rc29", "b2_rc30", "b2_rc31", "b2_rc32", "b2_rc33", "b2_rc34", "b2_rc35", "b2_rc36", "b2_rc37", "b2_rc38", "b2_rc39", "b2_rc40", "b2_rc41", "b2_rc42", "b2_rc43", "b2_rc44", "b2_rc45", "b2_rc46", "b2_rc47", "b2_rc48", "b2_rc49", "b2_rc50", "b2_rc51", "b2_rc52", "b2_rc53", "b2_rc54", "b2_rc55", "b2_rc56", "b2_rc57", "b2_rc58", "b2_rc59", "b2_rc60", "b2_rc61", "b2_rc62", "b2_rc63", "b2_rc64", "b2_rc65", "b2_rc66", "b2_rc67", "b2_rc68", "b2_rc69", "b2_rc70", "b2_rc71", "b2_rc72", "b2_rc73", "b2_rc74", "b2_rc75", "b2_rc76", "b2_rc77", "b2_rc78", "b2_rc79", "b2_rc80", "b2_rc81", "b2_rc82", "b2_rc83", "b2_rc84", "b2_rc85", "b2_rc86", "b2_rc87", "b2_rc88", "b2_rc89", "b2_rc90", "b2_rc91", "b2_rc92", "b2_rc93", "b2_rc94", "b2_rc95", "b2_rc96", "b2_rc97", "b2_rc98", "b2_rc99", "b2_rc100", "b2_rc101", "b2_rc102", "b2_rc103", "b2_rc104", "b2_rc105", "b2_rc106", "b2_rc107", "b2_rc108", "b2_rc109", "b2_rc110", "b2_rc111", "b2_rc112", "b2_rc113", "b2_rc114", "b2_rc115", "b2_rc116", "b2_rc117", "b2_rc118", "b2_rc119", "b2_rc120", "b2_rc121", "b2_rc122", "b2_rc123", "b2_rc124", "b2_rc125", "b2_rc126", "b2_rc127", "b2_rc128", "b2_rc129", "b2_rc130", "b2_rc131", "b2_rc132", "b2_rc133", "b2_rc134", "b2_rc135", "b2_rc136", "b2_rc137", "b2_rc138", "b2_rc139", "b2_rc140", "b2_rc141", "b2_rc142", "b2_rc143", "b2_rc144", "b2_rc145", "b2_rc146", "b2_rc147", "b2_rc148", "b2_rc149", "b2_rc150", "b2_rc151", "b2_rc152", "b2_rc153", "b2_rc154", "b2_rc155", "b2_rc156", "b2_rc157", "b2_rc158", "b2_rc159", "b2_rc160", "b2_rc161", "b2_rc162", "b2_rc163", "b2_rc164", "b2_rc165", "b2_rc166", "b2_rc167", "b2_rc168", "b2_rc169", "b2_rc170", "b2_rc171", "b2_rc172", "b2_rc173", "b2_rc174", "b2_rc175", "b2_rc176", "b2_rc177", "b2_rc178", "b2_rc179", "b2_rc180", "b2_rc181", "b2_rc182", "b2_rc183", "b2_rc184", "b2_rc185", "b2_rc186", "b2_rc187", "b2_rc188", "b2_rc189", "b2_rc190", "b2_rc191", "b2_rc192", "b2_rc193", "b2_rc194", "b2_rc195", "b2_rc196", "b2_rc197", "b2_rc198", "b2_rc199", "b2_rc200", "b2_rc201", "b2_rc202", "b2_rc203", "b2_rc204", "b2_rc205", "b2_rc206", "b2_rc207", "b2_rc208", "b2_rc209", "b2_rc210", "b2_rc211", "b2_rc212", "b2_rc213", "b2_rc214", "b2_rc215", "b2_rc216", "b2_rc217", "b2_rc218", "b2_rc219", "b2_rc220", "b2_rc221", "b2_rc222", "b2_rc223", "b2_rc224", "b2_rc225", "b2_rc226", "b2_rc227", "b2_rc228", "b2_rc229", "b2_rc230", "b2_rc231", "b2_rc232", "b2_rc233", "b2_rc234", "b2_rc235", "b2_rc236", "b2_rc237", "b2_rc238", "b2_rc239", "b2_rc240", "b2_rc241", "b2_rc242", "b2_rc243", "b2_rc244", "b2_rc245", "b2_rc246", "b2_rc247", "b2_rc248", "b2_rc249", "b2_rc250", "b2_rc251", "b2_rc252", "b2_rc253", "b2_rc254", "b2_rc255", "b2_rc256", "b2_rc257", "b2_rc258", "b2_rc259", "b2_rc260", "b2_rc261", "b2_rc262", "b2_rc263", "b2_rc264", "b2_rc265", "b2_rc266", "b2_rc267", "b2_rc268", "b2_rc269", "b2_rc270", "b2_rc271", "b2_rc272", "b2_rc273", "b2_rc274", "b2_rc275", "b2_rc276", "b2_rc277", "b2_rc278", "b2_rc279", "b2_rc280", "b2_rc281", "b2_rc282", "b2_rc283", "b2_rc284", "b2_rc285", "b2_rc286", "b2_rc287", "b2_rc288", "b2_rc289", "b2_rc290", "b2_rc291", "b2_rc292", "b2_rc293", "b2_rc294", "b2_rc295", "b2_rc296", "b2_rc297", "b2_rc298", "b2_rc299", "b2_rc300", "b2_rc301", 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