{ "_id": "6ac7926cde46216d5edd25f6", "Package": "SingscoreAMLMutations", "Title": "Using singscore to predict mutations in AML from transcriptomic\nsignatures", "Version": "1.29.0", "Authors@R": "c(\nperson(\n\"Dharmesh\",\n\"Bhuva\",\n\"D.\",\nemail = \"bhuva.d@wehi.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = '0000-0002-6398-9157')\n),\nperson(\n\"Momeneh\",\n\"Foroutan\",\nemail = \"foroutan.m@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0002-1440-0457')\n),\nperson(\n\"Yi\",\n\"Xie\",\nemail = \"xie.y@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0002-1938-4089')\n),\nperson(\n\"Ruqian\",\n\"Lyu\",\nemail = \"lyu.r@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '')\n),\nperson(\n\"Malvika\",\n\"Kharbanda\",\nemail = \"kharbanda.m@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0001-9726-3023')\n),\nperson(\n\"Joseph\",\n\"Cursons\",\nemail = \"cursons.j@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0002-5053-4540')\n),\nperson(\n\"Melissa\",\n\"Davis\",\n\"J.\",\nemail = \"davis.m@wehi.edu.au\",\nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0003-4864-7033')\n)\n)", "Description": "This workflow package shows how transcriptomic signatures\ncan be used to infer phenotypes. The workflow begins by showing\nhow the TCGA AML transcriptomic data can be downloaded and\nprocessed using the TCGAbiolinks packages. It then shows how\nsamples can be scored using the singscore package and\nsignatures from the MSigDB. Finally, the predictive capacity of\nscores in the context of predicting a specific mutation in AML\nis shown.The workflow exhibits the interplay of Bioconductor\npackages to achieve a gene-set level analysis.", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "true", "Workflow": "True", "biocViews": "GeneExpressionWorkflow, GenomicVariantsWorkflow,\nImmunoOncologyWorkflow, Workflow", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.0", "Language": "en-US", "URL": "https://github.com/DavisLaboratory/SingscoreAMLMutations", "BugReports": "https://github.com/DavisLaboratory/SingscoreAMLMutations/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:31 UTC", "RemoteUrl": "https://github.com/bioc/SingscoreAMLMutations", "RemoteRef": "HEAD", "RemoteSha": "933e8dab832779fa56b129b43399f4105fb43b40", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 12:44:29 UTC", "User": "root" }, "Author": "Dharmesh D. Bhuva [aut, cre] (ORCID:\n),\nMomeneh Foroutan [aut] (ORCID: ),\nYi Xie [aut] (ORCID: ),\nRuqian Lyu [aut],\nMalvika Kharbanda [aut] (ORCID:\n),\nJoseph Cursons [aut] (ORCID: ),\nMelissa J. Davis [aut] (ORCID: )", "Maintainer": "Dharmesh D. Bhuva ", "_user": "bioc", "_type": "src", "_file": "SingscoreAMLMutations_1.29.0.tar.gz", "_fileid": "https://r2.ropensci.org/c1d5ba92516ede108e7ac074add6d30000408df15a5c236b9f30806e602849b4", "_filesize": 153495, "_sha256": "c1d5ba92516ede108e7ac074add6d30000408df15a5c236b9f30806e602849b4", "_expires": "2027-01-16T12:54:02.000Z", "_created": "2026-10-08T12:44:29.000Z", "_published": "2026-10-08T12:54:04.642Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 2, "note": 5 }, "_upstream": "https://github.com/bioc/SingscoreAMLMutations", "_commit": { "id": "933e8dab832779fa56b129b43399f4105fb43b40", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380211 }, "_maintainer": { "name": "Dharmesh D. Bhuva", "email": "bhuva.d@wehi.edu.au", "orcid": "0000-0002-6398-9157" }, "_distro": "resolute", "_jobs": [ { "job": 113317540061, "time": 237, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11551228854" }, { "job": 113317540190, "time": 498, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11552000805" }, { "job": 113317540187, "time": 448, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11551459301" }, { "job": 113317539996, "time": 281, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11550928701" }, { "job": 113317540177, "time": 382, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11551538952" }, { "job": 113314009533, "time": 517, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11551600203" }, { "job": 113317539904, "time": 190, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11551118706" }, { "job": 113317540117, "time": 356, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11550664342" }, { "job": 113317540178, "time": 306, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11550999307" }, { "job": 113317540128, "time": 448, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11551034688" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dcanr", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "GSEABase", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "singscore", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "TCGAbiolinks", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "BiocWorkflowTools", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24", "repository": "workflows" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23", "repository": "workflows" } ], "_topics": [ "geneexpressionworkflow", "genomicvariantsworkflow", "immunooncologyworkflow", "workflow" ], "_stars": 1, "_contributors": [ { "user": "carissaxie", "count": 19, "uuid": 34535456 }, { "user": "hpages", "count": 10, "uuid": 8810451 }, { "user": "malvikakh", "count": 10, "uuid": 36639840 }, { "user": "jcursons", "count": 5, "uuid": 10367688 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 474, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/davislaboratory/singscoreamlmutations", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/SingscoreAMLMutations.html" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "AMLPatientMutationsTCGA", "title": "Mutation data for 4 genes for the TCGA AML patients", "object": "AMLPatientMutationsTCGA", "class": [ "data.frame" ], "fields": [ "NPM1c.Mut", "KMT2A.Fusion", "KMT2A.PTD", "PML.RARA" ], "rows": 151, "table": true, "tojson": true } ], "_help": [ { "page": "SingscoreAMLMutations-package", "title": "SingscoreAMLMutations: Using singscore to predict mutations in AML from transcriptomic signatures", "topics": [ "SingscoreAMLMutations-package", "SingscoreAMLMutations" ] }, { "page": "AMLPatientMutationsTCGA", "title": "Mutation data for 4 genes for the TCGA AML patients", "topics": [ "AMLPatientMutationsTCGA" ] } ], "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "cigarillo", "circlize", "cli", "clipr", "codetools", "colorspace", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "dcanr", "DelayedArray", "digest", "doRNG", "downloader", "dplyr", "edgeR", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "ggrepel", "GlobalOptions", "glue", "graph", "gridExtra", "GSEABase", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "openssl", "org.Hs.eg.db", "otel", "pillar", "pkgconfig", "plotly", "plyr", "png", "prettyunits", "progress", "promises", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "readr", "reshape", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "Rsamtools", "RSQLite", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "selectr", "Seqinfo", "shape", "singscore", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "TCGAbiolinks", "TCGAbiolinksGUI.data", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml" ], "_score": 3, "_indexed": true, "_nocasepkg": "singscoreamlmutations", "_universes": [ "bioc", "davislaboratory" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-10-08T12:49:59.000Z", "distro": "resolute", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/5c3c6438a11ebff8fa6ab407fd2255b391f9b967619510fcf59da32ca8a9a62b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.6.1", "os": "linux", "version": "1.29.0", "date": "2026-10-08T12:49:13.000Z", "distro": "resolute", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/2e345c529455eeba1c618c215a4c24503751443224e270da195221512498a5ca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-10-08T12:47:06.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/0435aa546da12cd491041c0259d87f8399de9b99cae21e313f369489dd9ab5a8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.6.1", "os": "mac", "version": "1.29.0", "date": "2026-10-08T12:47:49.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/cd793f8f2c5957e89c027af60549e84585816162cbb69f8a001862c99177b017", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-10-08T12:48:21.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/e9f2310edf575f493b8a2ccc6a5bd59ecefff5fda0bad4f139dcc5dccbb8211f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-10-08T12:47:30.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/4a563e136d70bb2c61f8f63e7c8510c617ebab9fd0e20087f46f12cfec2ab513", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-10-08T12:47:06.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/cecb9da4e544f4913dac238da5b4461720b613bab8732d582238e5d67695db68", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" }, { "r": "4.6.1", "os": "win", "version": "1.29.0", "date": "2026-10-08T12:49:06.000Z", "commit": "933e8dab832779fa56b129b43399f4105fb43b40", "fileid": "https://r2.ropensci.org/099806277f0eeb099e9871a5286c50e611f7ad266d8373e3f4cfb8793ad31d59", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37777945810" } ] }