{ "_id": "6ad0b19bf55ded6d77dfa543", "Package": "ComICS", "Title": "Computational Methods for Immune Cell-Type Subsets", "Description": "Provided are Computational methods for Immune Cell-type\nSubsets, including:(1) DCQ (Digital Cell Quantifier) to infer\nglobal dynamic changes in immune cell quantities within a\ncomplex tissue; and (2) VoCAL (Variation of Cell-type Abundance\nLoci) a deconvolution-based method that utilizes transcriptome\ndata to infer the quantities of immune-cell types, and then\nuses these quantitative traits to uncover the underlying DNA\nloci.", "Version": "1.0.4", "Authors@R": "c(person(\"Yael\", \"Steuerman\", email = \"yaelsteu@mail.tau.ac.il\", role = c(\"aut\", \"cre\")), person(\"Irit\", \"Gat-Viks\", email = \"iritgv@post.tau.ac.il\", role = \"aut\"))", "License": "GPL-2", "LazyData": "true", "URL": "http://dcq.tau.ac.il/ , http://csgi.tau.ac.il/VoCAL/", "RoxygenNote": "5.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 10:53:31 UTC", "User": "root" }, "Author": "Yael Steuerman [aut, cre], Irit Gat-Viks [aut]", "Maintainer": "Yael Steuerman ", "Repository": "https://yaelsteu.r-universe.dev", "Date/Publication": "2018-05-13 07:19:17 UTC", "RemoteUrl": "https://github.com/cran/ComICS", "RemoteRef": "HEAD", "RemoteSha": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "_user": "yaelsteu", "_type": "src", "_file": "ComICS_1.0.4.tar.gz", "_fileid": "https://r2.ropensci.org/005aeed6dcbbb181a57a0422d8559c605ba6e69ad2583f1285e2e9f16b92dd3b", "_filesize": 1053704, "_sha256": "005aeed6dcbbb181a57a0422d8559c605ba6e69ad2583f1285e2e9f16b92dd3b", "_expires": "2027-01-23T10:57:25.000Z", "_created": "2026-10-15T10:53:31.000Z", "_published": "2026-10-15T10:57:31.615Z", "_buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116383590878, "time": 109, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11967088455" }, { "job": 116383590738, "time": 168, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967240308" }, { "job": 116383590858, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11966314117" }, { "job": 116383590889, "time": 160, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11966508891" }, { "job": 116382378584, "time": 183, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11967128069" }, { "job": 116383590796, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11967285080" }, { "job": 116383590746, "time": 135, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11966848654" }, { "job": 116383590793, "time": 124, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11966508825" }, { "job": 116383590857, "time": 94, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11965594836" } ], "_upstream": "https://github.com/cran/ComICS", "_commit": { "id": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "author": "Yael Steuerman ", "committer": "cran-robot ", "message": "version 1.0.4\n", "time": 1526195957 }, "_maintainer": { "name": "Yael Steuerman", "email": "yaelsteu@mail.tau.ac.il", "login": "yaelsteu", "description": "", "uuid": 9842954 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "glmnet", "role": "Imports" }, { "package": "stats", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 3, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "yaelsteu", "count": 5, "uuid": 9842954 } ], "_userbio": { "uuid": 9842954, "type": "user", "name": "yaelsteu", "followers": 0 }, "_downloads": { "count": 1246, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ComICS" }, "_mentions": 2, "_searchresults": 32, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/ComICS.html", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "yaelsteu", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2015-12-09" }, { "version": "1.0.1", "date": "2015-12-14" }, { "version": "1.0.2", "date": "2016-01-28" }, { "version": "1.0.3", "date": "2016-03-07" }, { "version": "1.0.4", "date": "2018-05-13" } ], "_exports": [ "dcq", "vocal" ], "_datasets": [ { "name": ".combine_iQTL_association_scores", "title": "ComICS-internal", "object": "vocalEx", "class": [ "function" ], "fields": [], "table": false, "tojson": true }, { "name": ".fishersMethod", "title": "ComICS-internal", "object": "vocalEx", "class": [ "function" ], "fields": [], "table": false, "tojson": true }, { "name": ".iterative_filteration", "title": "ComICS-internal", "object": "vocalEx", "class": [ "function" ], "fields": [], "table": false, "tojson": true }, { "name": "DCQ_mar", "title": "Shared Immunological datasets", "object": "commons", "class": [ "data.frame" ], "fields": [ "DCQ" ], "rows": 61, "table": true, "tojson": true }, { "name": "eQTL_res", "title": "Example datasets for runnning vocal", "object": "vocalEx", "class": [ "matrix", "array" ], "fields": [], "rows": 61, "table": true, "tojson": true }, { "name": "gBXD", "title": "Example datasets for runnning vocal", "object": "vocalEx", "class": [ "data.frame" ], "fields": [ "Locus", "Chr", "Start_pos", "End_pos", "cM", "B6", "D2", "BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11", "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18", "BXD19", "BXD20", "BXD21", "BXD22", "BXD23", "BXD24", "BXD25", "BXD27", "BXD28", "BXD29", "BXD30", "BXD31", "BXD32", "BXD33", "BXD34", "BXD35", "BXD36", "BXD37", "BXD38", "BXD39", "BXD40", "BXD41", "BXD42", "BXD43", "BXD44", "BXD45", "BXD48", "BXD49", "BXD50", "BXD51", "BXD52", "BXD53", "BXD54", "BXD55", "BXD56", "BXD59", "BXD60", "BXD61", "BXD62", "BXD63", "BXD64", "BXD65", "BXD66", "BXD67", "BXD68", "BXD69", "BXD70", "BXD71", "BXD72", "BXD73", "BXD74", "BXD75", "BXD76", "BXD77", "BXD78", "BXD79", "BXD80", "BXD81", "BXD83", "BXD84", "BXD85", "BXD86", "BXD87", "BXD88", "BXD89", "BXD90", "BXD91", "BXD92", "BXD93", "BXD94", "BXD95", "BXD96", "BXD97", "BXD98", "BXD99", "BXD100", "BXD101", "BXD102", "BXD103" ], "rows": 3796, "table": true, "tojson": true }, { "name": "immgen_dat", "title": "Shared Immunological datasets", "object": "commons", "class": [ "data.frame" ], "fields": [], "rows": 61, "table": true, "tojson": true }, { "name": "lung_dat", "title": "Example datasets for runnning vocal", "object": "vocalEx", "class": [ "data.frame" ], "fields": [ "B6", "D2", "BXD97", "BXD84", "BXD87", "BXD1", "BXD12", "BXD62", "BXD83", "BXD2", "BXD55", "BXD50", "BXD40", "BXD56", "BXD100", "BXD51", "BXD48", "BXD70", "BXD39", "BXD98", "BXD16", "BXD32", "BXD45", "BXD21", "BXD66", "BXD6", "BXD68", "BXD34", "BXD27", "BXD90", "BXD60", "BXD69", "BXD71", "BXD65", "BXD25", "BXD14", "BXD9", "BXD96", "BXD42", "BXD33", "BXD43", "BXD19", "BXD31", "BXD22", "BXD86", "BXD99", "BXD73", "BXD75", "BXD89" ], "rows": 61, "table": true, "tojson": true }, { "name": "lung_time_series_dat", "title": "Example datasets for runnning dcq", "object": "dcqEx", "class": [ "data.frame" ], "fields": [ "000a_hour_delta", "000b_hour_delta", "000c_hour_delta", "000d_hour_delta", "003_hour_delta", "004_hour_delta", "007_hour_delta", "008_hour_delta", "011_hour_delta", "012_hour_delta", "026_hour_delta", "028_hour_delta", "032_hour_delta", "049_hour_delta", "050_hour_delta", "074_hour_delta", "075_hour_delta", "098_hour_delta", "099_hour_delta", "122_hour_delta", "123_hour_delta", "148_hour_delta", "149_hour_delta" ], "rows": 61, "table": true, "tojson": true } ], "_help": [ { "page": "ComICS", "title": "Computational methods for Immune Cell-type Subsets", "topics": [ "ComICS-package", "ComICS" ] }, { "page": "commons", "title": "Shared Immunological datasets", "topics": [ "DCQ_mar", "immgen_dat" ] }, { "page": "dcq", "title": "DCQ - Digital Cell Quantifier", "topics": [ "dcq" ] }, { "page": "dcqEx", "title": "Example datasets for runnning dcq", "topics": [ "lung_time_series_dat" ] }, { "page": "vocal", "title": "Variation in Cell Abundance Loci", "topics": [ "vocal" ] }, { "page": "vocalEx", "title": "Example datasets for runnning vocal", "topics": [ "eQTL_res", "gBXD", "lung_dat" ] } ], "_rundeps": [ "codetools", "foreach", "glmnet", "iterators", "lattice", "Matrix", "Rcpp", "RcppEigen", "shape", "survival" ], "_score": 2.855940525746363, "_indexed": true, "_nocasepkg": "comics", "_universes": [ "yaelsteu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-10-15T10:55:17.000Z", "distro": "resolute", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/435d094da1b3afeaa990dc1c023dd392d2399a201af22d1574c20d6620fd7d2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.6.1", "os": "linux", "version": "1.0.4", "date": "2026-10-15T10:56:23.000Z", "distro": "resolute", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/c7e5a1eb997da63c90b465221b91a344cb8a23e17ccaa22fe1c256816e2f8bbe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-10-15T10:56:23.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/a125ae6d43d33f313af765edf869010be4a309200396fbbb2b87f07ec602ee8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.6.1", "os": "mac", "version": "1.0.4", "date": "2026-10-15T10:55:59.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/96a78e939f65255be059deeb75c973d621e99c93e2c650d93913372772b01509", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.4", "date": "2026-10-15T10:55:52.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/d916a02303cf5ff26dfef60f7681ef12cd604182bf3a71202a490d94736ed0cf", "status": "success", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.7.0", "os": "win", "version": "1.0.4", "date": "2026-10-15T10:55:49.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/c8d548ad515cb7dd28e7cf674c5a6b87f63c4682064938ce1ce983641e173ed8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.5.3", "os": "win", "version": "1.0.4", "date": "2026-10-15T10:55:27.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/d53328df394fa4eec5393d57264248c98db5013c2196871c4565998869e39056", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" }, { "r": "4.6.1", "os": "win", "version": "1.0.4", "date": "2026-10-15T10:55:12.000Z", "commit": "3e0b1f9fcc5d5b0ce868ce5ae95eedca66f1f840", "fileid": "https://r2.ropensci.org/cf429df5565ff5f018adbfbe2e4e51c0149956dcefe0de66044e757b699d9604", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yaelsteu/actions/runs/38723099955" } ] }