{ "_id": "6a1ee170b401979e734109fe", "Package": "mastR", "Title": "Markers Automated Screening Tool in R", "Version": "1.13.1", "Authors@R": "c(\nperson(\"Jinjin\", \"Chen\", email = \"chen.j@wehi.edu.au\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7923-5723\")),\nperson(\"Ahmed\", \"Mohamed\", email = \"mohamed.a@wehi.edu.au\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0001-6507-5300\")),\nperson(\"Chin Wee\", \"Tan\", email = \"cwtan@wehi.edu.au\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-9695-7218\"))\n)", "Description": "mastR is an R package designed for automated screening of\nsignatures of interest for specific research questions. The\npackage is developed for generating refined lists of signature\ngenes from multiple group comparisons based on the results from\nedgeR and limma differential expression (DE) analysis workflow.\nIt also takes into account the background noise of\ntissue-specificity, which is often ignored by other marker\ngeneration tools. This package is particularly useful for the\nidentification of group markers in various biological and\nmedical applications, including cancer research and\ndevelopmental biology.", "biocViews": "Software, GeneExpression, Transcriptomics,\nDifferentialExpression, Visualization", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Collate": "'plot.R' 'DE_functions.R' 'AllGenerics.R'\n'filter_subset_sig-methods.R' 'get_de_table-methods.R'\n'get_degs-methods.R' 'get_gsc_sig-methods.R' 'get_lm_sig.R'\n'get_panglao_sig.R' 'gls2gsc-methods.R' 'gsc_plot.R'\n'list_panglao_organs.R' 'list_panglao_types.R'\n'mastR-package.R' 'merge_markers.R' 'pca_matrix_plot-methods.R'\n'pseudo_samples-methods.R' 'remove_bg_exp-methods.R'\n'sig_boxplot-methods.R' 'sig_gseaplot-methods.R'\n'sig_heatmap-methods.R' 'sig_rankdensity_plot-methods.R'\n'sig_scatter_plot-methods.R' 'subset_sig_by_step.R'", "URL": "https://davislaboratory.github.io/mastR", "BugReports": "https://github.com/DavisLaboratory/mastR/issues", "VignetteBuilder": "knitr", "Language": "en-US", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-20 01:58:30 UTC", "RemoteUrl": "https://github.com/bioc/mastR", "RemoteRef": "HEAD", "RemoteSha": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 06:54:26 UTC", "User": "root" }, "Author": "Jinjin Chen [aut, cre] (ORCID: ),\nAhmed Mohamed [aut, ctb] (ORCID:\n),\nChin Wee Tan [ctb] (ORCID: )", "Maintainer": "Jinjin Chen ", "MD5sum": "fc5411e691bda0145ff7980511ae60cc", "_user": "bioc", "_type": "src", "_file": "mastR_1.13.1.tar.gz", "_fileid": "529d3215d4aad788ad58ad36db23d10283f69a9dbad98371519826640c96a0eb", "_filesize": 4684247, "_sha256": "529d3215d4aad788ad58ad36db23d10283f69a9dbad98371519826640c96a0eb", 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PanglaoDB website.", "topics": [ "get_panglao_sig" ] }, { "page": "gls2gsc", "title": "Convert gene-set list into GeneSetCollection", "topics": [ "gls2gsc", "gls2gsc,list-method", "gls2gsc,vector-method" ] }, { "page": "gsc_plot", "title": "Make upset plot for given gene sets", "topics": [ "gsc_plot" ] }, { "page": "im_data_6", "title": "RNA-seq TMM normalized counts data of 6 sorted immune subsets.", "topics": [ "im_data_6" ] }, { "page": "list_panglao_organs", "title": "Show the summary info of available organs in PanglaoDB.", "topics": [ "list_panglao_organs" ] }, { "page": "list_panglao_types", "title": "Show the summary info of available cell types in PanglaoDB.", "topics": [ "list_panglao_types" ] }, { "page": "lm22", "title": "LM22 matrix for CIBERSORT.", "topics": [ "lm22" ] }, { "page": "lm7", "title": "LM7 matrix for CIBERSORT.", "topics": [ "lm7" ] }, { "page": "merge_markers", "title": "Merge markers list into one.", "topics": [ "merge_markers" ] }, { "page": 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Customized contrast matrix", "2. Process data", "3. Results", "Visualization", "Session Info" ], "created": "2026-01-05 01:16:39", "modified": "2026-05-20 01:27:23", "commits": 3 }, { "source": "mastR_Demo.Rmd", "filename": "mastR_Demo.html", "title": "mastR: Markers Automated Screening Tool in R", "author": "Jinjin Chen, Ahmed Mohamed, Chin Wee Tan", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step 1. Build Markers Pool", "Generate Markers from Sources", "i) Leukocyte gene signature Matrix (LM)", "ii) MSigDB", "iii) PanglaoDB", "iv) Customized gene list", "Pool Markers from Sources", "Step 2. Signature Identification for Target Group", "a) data processing", "b) signature selection based on differential expression", "c) constrain signature within markers pool", "Step 3. Signature Refinement by Background Expression in Tissue", "I) data subsetting", "II) data filtration", "III) markers pool refinement", "use CCLE as background data (optional)", "IV) combination with Signature", "Step 4. Visualization of Final Results", "Heatmap", "Signature Score Boxplot", "Signature Abundance Scatter Plot", "Signature GSEA plot", "Working with Extension Data Input", "Multiple Datasets", "Single Cell RNA-sequencing Data", "Applications", "Score", "Deconvolution", "Annotation", "Session Info" ], "created": "2023-02-17 07:57:01", "modified": "2025-07-01 02:48:34", "commits": 38 } ], "_score": 5.778151250383644, "_indexed": true, "_nocasepkg": "mastr", "_universes": [ "bioc", "gene233", "davislaboratory" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.1", "date": "2026-05-20T07:00:12.000Z", "distro": "noble", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "aece9dcd9a7a891afc81b99dbe951953d6f2ad62e99002091999fea1a56bd90a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.6.0", "os": "linux", "version": "1.13.1", "date": "2026-05-20T07:00:27.000Z", "distro": "noble", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "a3dcd5eddd39d3a2573101e665af04b2c18dc162e32affa4f926b99afcb307fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.5.3", "os": "mac", "version": "1.13.1", "date": "2026-05-20T06:58:48.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "ca995f778daebc1d493a6dbff5a0de0b5622a28c49dc10df24873536c8934e79", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.6.0", "os": "mac", "version": "1.13.1", "date": "2026-05-20T06:58:31.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "53d161dd383591dce12d8aefbcc41f5cc823bffeffc6702c6fa414965a4b9141", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.7.0", "os": "win", "version": "1.13.1", "date": "2026-05-20T06:58:37.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "2886ab1b31a42fe78d86240d3ad0d5294afd98dc1fc7d9f6682a03d1fdd1fe56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.5.3", "os": "win", "version": "1.13.1", "date": "2026-05-20T06:59:21.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "0b4bb81f9d59ef33f887b171c368da78b44675c3f36e93df5e0ebd0fd7af8fef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.6.0", "os": "win", "version": "1.13.1", "date": "2026-05-20T06:58:25.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "6b7fa6a7582659af92d7e74b690429bb775671d2289271a0e0d098a1ea5e8400", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.1", "date": "2026-06-02T13:57:17.000Z", "commit": "1e1d3c67119589e38a251e1316ba92d4acc6e4d8", "fileid": "fbcebddd1b98c896ce64f4ee9a8d214d023cbf3c31764ae27c46f566ecbe50ca", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26146256595" } ] }