{ "_id": "6acb4503fe5cc25786e8d2c7", "Package": "UNDO", "Type": "Package", "Title": "Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions", "Version": "1.55.0", "Date": "2014-07-17", "Author": "Niya Wang ", "Maintainer": "Niya Wang ", "biocViews": "Software", "Description": "UNDO is an R package for unsupervised deconvolution of\ntumor and stromal mixed expression data. It detects marker\ngenes and deconvolutes the mixing expression data without any\nprior knowledge.", "License": "GPL-2", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:51 UTC", "RemoteUrl": "https://github.com/bioc/UNDO", "RemoteRef": "HEAD", "RemoteSha": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-11 07:53:55 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "UNDO_1.55.0.tar.gz", "_fileid": "https://r2.ropensci.org/eea4f5a0d61832fb708b2e170dfc8e0d89ed9301a650fb9cf4b9ac0fa844423a", "_filesize": 3028147, "_sha256": "eea4f5a0d61832fb708b2e170dfc8e0d89ed9301a650fb9cf4b9ac0fa844423a", "_expires": "2027-01-19T08:12:49.000Z", "_created": "2026-10-11T07:53:55.000Z", "_published": "2026-10-11T08:12:51.392Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 3, "warning": 2, "note": 11 }, "_upstream": "https://github.com/bioc/UNDO", "_commit": { "id": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379931 }, "_maintainer": { "name": "Niya Wang", "email": "wangny@vt.edu" }, "_distro": "resolute", "_jobs": [ { "job": 114421244874, "time": 115, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11695408670" }, { "job": 114421244912, "time": 148, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11696470612" }, { "job": 114421244953, "time": 150, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11695109032" }, { "job": 114421244947, "time": 96, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11696427363" }, { "job": 114421244944, "time": 104, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11696147943" }, { "job": 114420761600, "time": 173, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11695528574" }, { "job": 114421244907, "time": 72, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11696560479" }, { "job": 114421244935, "time": 88, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11696565441" }, { "job": 114421244965, "time": 75, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11695778241" }, { "job": 114421244960, "time": 68, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11696365732" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.2", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "MASS", "role": "Imports" }, { "package": "boot", "role": "Imports" }, { "package": "nnls", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.55.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.54.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 555, "source": "https://www.bioconductor.org/packages/stats/bioc/UNDO" }, "_mentions": 5, "_searchresults": 6, "_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/UNDO.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calc_E1", "dimension_reduction", "gene_expression_input", "marker_gene_selection", "mixing_matrix_computation", "two_source_deconv" ], "_datasets": [ { "name": "BiologicalMixMCF7HS27", "title": "MCF7 and HS27 biologically mixed", "object": "BiologicalMixMCF7HS27", "file": "BiologicalMixMCF7HS27.rda", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false }, { "name": "NumericalMixingMatrix", "title": "mixing matrix of data NumericalMixMCF7HS27", "object": "NumericalMixingMatrix", "file": "NumericalMixingMatrix.rda", "class": [ "matrix", "array" ], "fields": [ "V1", "V2" ], "rows": 2, "table": true, "tojson": true }, { "name": "NumericalMixMCF7HS27", "title": "MCF7 and HS27 numerically mixed", "object": "NumericalMixMCF7HS27", "file": "NumericalMixMCF7HS27.rda", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false }, { "name": "PureMCF7HS27", "title": "pure MCF7 and HS27", "object": "PureMCF7HS27", "file": "PureMCF7HS27.rda", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "UNDO-package", "title": "Implementation of UNDO (unsupervised deconvolution of tumor-stromal mixed expressions)", "topics": [ "UNDO-package", "UNDO" ] }, { "page": "BiologicalMixMCF7HS27", "title": "MCF7 and HS27 biologically mixed", "topics": [ "BiologicalMixMCF7HS27" ] }, { "page": "calc_E1", "title": "function calculating the E1 measurement", "topics": [ "calc_E1" ] }, { "page": "dimension_reduction", "title": "Dimension reduction function", "topics": [ "dimension_reduction" ] }, { "page": "gene_expression_input", "title": "Detect whether the input gene expression data are valid", "topics": [ "gene_expression_input" ] }, { "page": "marker_gene_selection", "title": "Select marker genes in two sources", "topics": [ "marker_gene_selection" ] }, { "page": "mixing_matrix_computation", "title": "Calculate and scale the mixing matrix", "topics": [ "mixing_matrix_computation" ] }, { "page": "NumericalMixingMatrix", "title": "mixing matrix of data NumericalMixMCF7HS27", "topics": [ "NumericalMixingMatrix" ] }, { "page": "NumericalMixMCF7HS27", "title": "MCF7 and HS27 numerically mixed", "topics": [ "NumericalMixMCF7HS27" ] }, { "page": "PureMCF7HS27", "title": "pure MCF7 and HS27", "topics": [ "PureMCF7HS27" ] }, { "page": "two_source_deconv", "title": "Main function to call other subfunction to deconvolute the mixed expression data.", "topics": [ "two_source_deconv" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "boot", "generics", "MASS", "nnls" ], "_vignettes": [ { "source": "UNDO-vignette.Rnw", "filename": "UNDO-vignette.pdf", "title": "UNDO Usage", "engine": "utils::Sweave", "headings": [], "created": "2014-03-20 23:55:49", "modified": "2014-07-17 21:21:51", "commits": 3 } ], "_score": 4, "_indexed": true, "_nocasepkg": "undo", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.55.0", "date": "2026-10-11T07:56:18.000Z", "distro": "resolute", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/4bbd7accf40d1c4a863e62efe8e1419efa9270db1be5b306d4ceb6bc05d8bbe3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.6.1", "os": "linux", "version": "1.55.0", "date": "2026-10-11T07:56:30.000Z", "distro": "resolute", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/3b293649793ebfcecca3146fc4009a3951c932a32e5e3b62bb669c531ffaf40f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.5.3", "os": "mac", "version": "1.55.0", "date": "2026-10-11T08:11:25.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/c5f3591e409c28f23769386bff44b87844d8bd1a3400d11b2c66794b01c19a77", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.6.1", "os": "mac", "version": "1.55.0", "date": "2026-10-11T08:12:05.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/0da29ad3a3e9e2d916ffe82f6d061dc11a9ed38df5391190655382b10f2730eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.6.0", "os": "wasm", "version": "1.55.0", "date": "2026-10-11T07:55:23.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/3627b3308115ba58771784dbd971a3cb5bc0e1f43b864b89337a9c51f2d08e19", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.7.0", "os": "win", "version": "1.55.0", "date": "2026-10-11T07:55:08.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/b17da022319b3d65db56ef9c031e0caa4d0a88c22ed31eef01548079d50784d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.5.3", "os": "win", "version": "1.55.0", "date": "2026-10-11T07:55:01.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/239157942142d4a69f2c42b741c8bda290db9a2f3e6d9dc4d69e04fbdc632b16", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" }, { "r": "4.6.1", "os": "win", "version": "1.55.0", "date": "2026-10-11T07:54:54.000Z", "commit": "69dc91341901a7ecd5819ed55c8cc44f2aefad54", "fileid": "https://r2.ropensci.org/6e1ec743b6c90710c10fcfcfc8d4689273c9c3e847fdaf1e4ea6f1a6c396a2de", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38122759676" } ] }