{ "_id": "6a1ac20e1d7bb097a09d948c", "Package": "MethPed", "Type": "Package", "Version": "1.41.0", "Date": "2016-01-01", "Title": "A DNA methylation classifier tool for the identification of\npediatric brain tumor subtypes", "Authors@R": "c( person(given = \"Mohammad Tanvir\", family = \"Ahamed\", role\n= c(\"aut\",\"trl\")), person(given = \"Anna\", family =\n\"Danielsson\", role = \"aut\"), person(given = \"Szilárd\", family =\n\"Nemes\", role = c(\"aut\",\"trl\")), person(given = \"Helena\",\nfamily = \"Carén\", role = c(\"aut\",\"cre\",\"cph\"),email =\n\"helenacarenlab@gmail.com\"))", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, DNAMethylation, Classification, Epigenetics", "Encoding": "UTF-8", "Description": "Classification of pediatric tumors into biologically\ndefined subtypes is challenging and multifaceted approaches are\nneeded. For this aim, we developed a diagnostic classifier\nbased on DNA methylation profiles. We offer MethPed as an\neasy-to-use toolbox that allows researchers and clinical\ndiagnosticians to test single samples as well as large cohorts\nfor subclass prediction of pediatric brain tumors. The current\nversion of MethPed can classify the following tumor\ndiagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG),\nEpendymoma, Embryonal tumors with multilayered rosettes (ETMR),\nGlioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3),\nGroup 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and\nPilocytic Astrocytoma (PiloAstro).", "License": "GPL-2", "RoxygenNote": "5.0.1", "NeedsCompilation": "no", "Author": "Mohammad Tanvir Ahamed [aut, trl], Anna Danielsson [aut],\nSzilárd Nemes [aut, trl], Helena Carén [aut, cre, cph]", "Maintainer": "Helena Carén ", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:50 UTC", "RemoteUrl": "https://github.com/bioc/MethPed", "RemoteRef": "HEAD", "RemoteSha": "acad6ae20b2dbfac00b54e90fbf54989e471d564", "Packaged": { "Date": "2026-05-30 07:34:32 UTC", "User": "root" }, "MD5sum": "2f7d30ca2c54946f6a7e1106e78e8956", "_user": "bioc", "_type": "src", "_file": "MethPed_1.41.0.tar.gz", "_fileid": 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"helenacarenlab@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "randomForest", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "impute", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "dnamethylation", "classification", "epigenetics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": 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], "_help": [ { "page": "checkNA", "title": "Check missing valus in dataset", "topics": [ "checkNA" ] }, { "page": "MethPed", "title": "MethPed: a DNA methylation classifier tool for the identification of pediatric brain tumor subtypes.", "topics": [ "MethPed" ] }, { "page": "MethPed_900probes", "title": "List of 900 probes in the predictor data", "topics": [ "MethPed_900probes" ] }, { "page": "MethPed_sample", "title": "Sample dataset to MethPed package.", "topics": [ "MethPed_sample" ] }, { "page": "plot.methped", "title": "Plot conditional probability of samples that belongs to different tumor subtypes.", "topics": [ "plot.methped" ] }, { "page": "probeMis", "title": "Missing probe names from training data compared with input samples.", "topics": [ "probeMis" ] }, { "page": "summary.methped", "title": "Summary of conditional probability or binary classification of samples that belong to different tumor subtypes.", "topics": [ "summary.methped" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics", "randomForest" ], "_vignettes": [ { "source": "MethPed-vignette.Rmd", "filename": "MethPed-vignette.html", "title": "__MethPed__A DNA Methylation Classifier Tool for the Identification of Pediatric Brain Tumor Subtypes", "author": "*Mohammad Tanvir Ahamed, Anna Danielsson, Szilárd Nemes and Helena Carén*University of Gothenburg, Sweden", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Necessary packages and installation guide", "Input data type and format for the MethPed classifier", "Input data type", "Input data format", "ExpressionSet class", "matrix class", "data.frame class", "Workflow of MethPed classifier", "A working example of MethPed", "Dataset without missing probe values", "Check missing value in data", "Apply the MethPed classifier", "Output summary", "Output visualization", "Count missing probes", "Dataset with missing probe values", "Missing beta value in the data set", "Missing values imputation", "Contact and Citation", "Contact", "Citation", "Authors information", "Session info", "References" ], "created": "2016-03-06 08:27:26", "modified": "2018-08-30 17:52:04", "commits": 2 } ], "_score": 4, "_indexed": true, "_nocasepkg": "methped", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T07:38:09.000Z", "distro": "noble", "commit": "acad6ae20b2dbfac00b54e90fbf54989e471d564", "fileid": "8a70fb9ceceb01398f33a49c264c6a268b57b3e58c3380ecf1160fc77f3ff3ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678124498" }, { "r": "4.6.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T07:37:00.000Z", "distro": "noble", "commit": "acad6ae20b2dbfac00b54e90fbf54989e471d564", "fileid": "4e4a2565053d52cd7bb55b48c3e8d0c78cd603c48deaba4c91612872ef5f80ea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678124498" }, { "r": "4.5.3", "os": "mac", 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