{ "_id": "6a1b05661d7bb097a0a03113", "Package": "TOAST", "Type": "Package", "Title": "Tools for the analysis of heterogeneous tissues", "Version": "1.26.0", "Description": "This package is devoted to analyzing high-throughput data\n(e.g. gene expression microarray, DNA methylation microarray,\nRNA-seq) from complex tissues. Current functionalities include\n1. detect cell-type specific or cross-cell type differential\nsignals 2. tree-based differential analysis 3. improve variable\nselection in reference-free deconvolution 4. partial\nreference-free deconvolution with prior knowledge.", "Author": "Ziyi Li and Weiwei Zhang and Luxiao Chen and Hao Wu", "Maintainer": "Ziyi Li ", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "false", "biocViews": "DNAMethylation, GeneExpression, DifferentialExpression,\nDifferentialMethylation, Microarray, GeneTarget, Epigenetics,\nMethylationArray", "BugReports": "https://github.com/ziyili20/TOAST/issues", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:48:12 UTC", "User": "root" }, "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:50:25 UTC", "RemoteUrl": "https://github.com/bioc/TOAST", "RemoteRef": "RELEASE_3_23", "RemoteSha": "b38dcc60eff89cba2727dd7c1242978227a6742c", "MD5sum": "a8fcb06a63fe6ba1e37de1d0471ff8c1", "_user": "bioc-release", "_type": "src", "_file": "TOAST_1.26.0.tar.gz", "_fileid": "cf503f43c77392e684636a8da7d6f6a56e2cfab911301f25bfd07bd338b834fa", "_filesize": 3777721, "_sha256": "cf503f43c77392e684636a8da7d6f6a56e2cfab911301f25bfd07bd338b834fa", "_created": "2026-05-30T10:48:12.000Z", "_published": "2026-05-30T15:42:30.263Z", "_jobs": [ { "job": 78643670414, "time": 187, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307681687" }, { "job": 78643670413, "time": 392, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307700778" }, { "job": 78643670412, "time": 448, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307706492" }, { "job": 78643670433, "time": 264, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309337978" }, { "job": 78643670421, "time": 258, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309336750" }, { "job": 78641272220, "time": 303, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307630711" }, { "job": 78643670409, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307675278" }, { "job": 78643670428, "time": 286, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307689770" }, { "job": 78643670416, "time": 326, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307693368" }, { "job": 78643670436, "time": 325, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307693273" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/TOAST", "_commit": { "id": "b38dcc60eff89cba2727dd7c1242978227a6742c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380625 }, "_maintainer": { "name": "Ziyi Li", "email": "zli16@mdanderson.org", "login": "ziyili20", "description": "", "uuid": 24440640 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "EpiDISH", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "nnls", "role": "Depends" }, { "package": "quadprog", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "gplots", "role": "Suggests" }, { "package": "matrixStats", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "dnamethylation", "geneexpression", "differentialexpression", "differentialmethylation", "microarray", "genetarget", "epigenetics", "methylationarray" ], "_stars": 14, "_contributors": [ { "user": "ziyili20", "count": 57, "uuid": 24440640 }, { "user": "nturaga", "count": 12, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1078, "source": "https://www.bioconductor.org/packages/stats/bioc/TOAST" }, "_mentions": 174, "_devurl": "https://github.com/ziyili20/toast", "_searchresults": 123, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/TOAST.html", "manual.pdf" ], "_homeurl": "https://github.com/ziyili20/toast", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assignCellType", "cedar", "ChooseMarker", "csDeconv", "csTest", "DEVarSelect", "findRefinx", "fitModel", "GetPrior", "makeDesign", "MDeconv", "myprojectMix", "myRefFreeCellMix", "myRefFreeCellMixInitialize", "plotCorr", "Tsisal" ], "_datasets": [ { "name": "beta_emp", "title": "Simulated methylation 450K array data with related", "object": "beta_emp", "file": "beta_emp.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "CBS_PBMC_array", "title": "An example dataset for partial reference-free cell composition estimation from tissue gene expression", "object": "CBS_PBMC_array", "file": "CBS_PBMC_array.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "RA_100samples", "title": "An example dataset for cellular proportion estimation and multiple factor design", "object": "RA_100samples", "file": "RA_100samples.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "assignCellType", "title": "Align cell types when reference proportions are known", "topics": [ "assignCellType" ] }, { "page": "beta_emp", "title": "Simulated methylation 450K array data with related", "topics": [ "beta_emp" ] }, { "page": "CBS_PBMC_array", "title": "An example dataset for partial reference-free cell composition estimation from tissue gene expression", "topics": [ "CBS_PBMC_array" ] }, { "page": "cedar", "title": "Testing cell type specific differential signals for specified phenotype by considering DE/DM state corrleation between cell types.", "topics": [ "cedar" ] }, { "page": "ChooseMarker", "title": "Choose cell type-specific markers from pure cell type profiles or single cell data", "topics": [ "ChooseMarker" ] }, { "page": "csDeconv", "title": "Improve reference-free deconvolution using cross-cell type differential analysis", "topics": [ "csDeconv" ] }, { "page": "csTest", "title": "Testing differential signals for specified phenotype and cell type(s).", "topics": [ "csTest" ] }, { "page": "DEVarSelect", "title": "Feature selection for reference-free deconvolution using cross-cell type differential analysis", "topics": [ "DEVarSelect" ] }, { "page": "findRefinx", "title": "findRefinx", "topics": [ "findRefinx" ] }, { "page": "fitModel", "title": "Fit model with proportions and phenotypes.", "topics": [ "fitModel" ] }, { "page": "GetPrior", "title": "Get prior knowledge for supported tissue types", "topics": [ "GetPrior" ] }, { "page": "makeDesign", "title": "Generate design matrix from input phenotypes and proportions.", "topics": [ "makeDesign" ] }, { "page": "MDeconv", "title": "Estimate cell compoisitons via partial reference-free deconvolution.", "topics": [ "MDeconv" ] }, { "page": "myprojectMix", "title": "Replicate the function myprojectMix() from RefFreeEWAS package", "topics": [ "myprojectMix" ] }, { "page": "myRefFreeCellMix", "title": "Replicate the function RefFreeCellMix() from RefFreeEWAS package", "topics": [ "myRefFreeCellMix" ] }, { "page": "myRefFreeCellMixInitialize", "title": "Replicate the function RefFreeCellMixInitialize() from RefFreeEWAS package", "topics": [ "myRefFreeCellMixInitialize" ] }, { "page": "plotCorr", "title": "Show DE/DM state correlation between cell types", "topics": [ "plotCorr" ] }, { "page": "RA_100samples", "title": "An example dataset for cellular proportion estimation and multiple factor design", "topics": [ "RA_100samples" ] }, { "page": "Tsisal", "title": "Complete Deconvolution of DNA methylation data based on TOAST and SISAL", "topics": [ "Tsisal" ] } ], "_readme": "https://github.com/bioc/TOAST/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "class", "cli", "codetools", "corpcor", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "doParallel", "dplyr", "e1071", "EpiDISH", "farver", "fastmap", "forcats", "foreach", "genefilter", "generics", "GenomicRanges", "GGally", "ggplot2", "ggstats", "glue", "gtable", "hms", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "limma", "locfdr", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnls", "openssl", "patchwork", "pillar", "pkgconfig", "png", "prettyunits", "progress", "proxy", "purrr", "quadprog", "R6", "RColorBrewer", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "TOAST.Rmd", "filename": "TOAST.html", "title": "Analyses of high-throughput data from heterogeneous samples with TOAST", "author": "Ziyi Li, Hao Wu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation and quick start", "Install TOAST", "How to get help for TOAST", "Quick start on detecting cell type-specific differential signals", "Example dataset", "Estimate mixing proportions", "Reference-based deconvolution using least square method", "Reference-free deconvolution using RefFreeEWAS", "Improve reference-free deconvolution with cross-cell type differential analysis", "Improved-RF with myRefFreeCellMix", "Improved-RF with use-defined RF function", "Partial reference-free deconvolution (TOAST/-P and TOAST/+P)", "Choose cell type-specific markers", "PRF deconvolution without prior (TOAST/-P)", "PRF deconvolution with prior (TOAST/+P)", "Complete deconvolution using a geometric approach", "Detect cell type-specific and cross-cell type differential signals", "Detect cell type-specific differential signals under two-group comparison", "Testing one parameter (e.g. disease) in one cell type.", "Testing one parameter in all cell types.", "Testing one parameter in all cell types by incorporating DE/DM state correlation among cell types", "Detect cell type-specific differential signals from a general experimental design", "Testing one parameter in one cell type", "Testing the joint effect of single parameter in all cell types.", "Detect cross-cell type differential signals", "Testing cross-cell type differential signals in cases (or in controls).", "Testing the overall cross-cell type differences in all samples.", "Testing the differences of two cell types over different values of one phenotype (higher-order test).", "A few words about variance bound and Type I error.", "Variance bound", "Type I error", "Session info" ], "created": "2019-05-21 01:03:29", "modified": "2022-08-14 17:01:06", "commits": 9 } ], "_score": 8.34783315401598, "_indexed": false, "_nocasepkg": "toast", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/TOAST", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-05-30T10:56:59.000Z", "distro": "noble", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "4682693e3dce0ee6c41c6108d9ddbef8ad71c351e933f2cba01b8fa65c7ac9b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.6.0", "os": "linux", "version": "1.26.0", "date": "2026-05-30T10:57:36.000Z", "distro": "noble", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "79f8fdb66e457c8a25cf524b3dd8a62613fe71c331691365c50b1a891608403e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.5.3", "os": "mac", "version": "1.26.0", "date": "2026-05-30T15:39:16.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "f32b313b43d7ef0c3756c2caf5b9c60cbe5eb9b7ea388894b719ccc95feeeda3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.6.0", "os": "mac", "version": "1.26.0", "date": "2026-05-30T15:39:02.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "106c340d70fb661c0182d0e905b5948d589dd633668a2d9e8432ec671d45a7fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.6.0", "os": "wasm", "version": "1.26.0", "date": "2026-05-30T10:56:23.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "5aac9f232946ddc5da029c379fd1511e142dcbac2fd3ff7d54554d8e06211db7", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.7.0", "os": "win", "version": "1.26.0", "date": "2026-05-30T10:55:30.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "79e59a5f9b82c485dccbc8a04edc0efb62daed0e9f706b66ad0afa9e28d8cafa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.5.3", "os": "win", "version": "1.26.0", "date": "2026-05-30T10:55:19.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "e9b4d57cc2599010141dd182b28b58b136a2d0230c57c82ffee7b42759f1811d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" }, { "r": "4.6.0", "os": "win", "version": "1.26.0", "date": "2026-05-30T10:55:43.000Z", "commit": "b38dcc60eff89cba2727dd7c1242978227a6742c", "fileid": "830b2a921b1bca5996c2ed13d93426a826e813b5efbd02d6a9354b6ec206bfaf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680471984" } ] }