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Phosphorylated Sites (SPSs)", "topics": [ "SPSs" ] }, { "page": "standardise", "title": "Standardisation", "topics": [ "standardise" ] }, { "page": "tImpute", "title": "Tail-based impute", "topics": [ "tImpute" ] } ], "_readme": "https://github.com/bioc/PhosR/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "Biobase", "BiocGenerics", "boot", "broom", "car", "carData", "circlize", "class", "cli", "coda", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "crayon", "curl", "DelayedArray", "dendextend", "Deriv", "doBy", "dplyr", "e1071", "farver", "forcats", "forecast", "Formula", "fracdiff", "generics", "GenomicRanges", "GGally", "ggdendro", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggstats", "ggtext", "GlobalOptions", "glue", "gridExtra", "gridtext", "gtable", "hms", "igraph", "IRanges", "isoband", "jpeg", "labeling", "lattice", "lifecycle", "limma", "litedown", "lme4", "lmtest", "magrittr", "markdown", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", 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packages and data", "Setting up the PhosphoExperiment object", "Part A. Preprocessing", "Imputation", "Setting up the data", "Filtering of phosphosites", "Imputation of phosphosites", "Site- and condition-specific imputation", "Paired tail-based imputation", "Quantification plots", "Batch correction", "Diagnosing batch effect", "Correcting batch effect", "Quality control", "Generating SPSs", "Part B. Downstream analysis", "Pathway analysis", "1-dimensional enrichment analysis", "Prepare the Reactome annotation", "Perform 1D gene-centric pathway analysis", "2- and 3-dimensional signalling pathway analysis", "Site- and gene- centric analysis", "Gene-centric analyses of the liver phosphoproteome data", "Site-centric analyses of the liver phosphoproteome data", "Signalomes", "Generation of kinase-substrate relationship scores", "Signalome construction", "Generate signalome map", "Generate signalome network", "Session Info" ], "created": "2020-06-30 00:48:25", "modified": "2021-04-23 12:47:59", "commits": 19 } ], "_score": 5.296665190261531, "_indexed": true, "_nocasepkg": "phosr", "_universes": [ "bioc", "dixiao3447" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:27:22.000Z", "distro": "noble", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "b0fc4fe98f6a90a5037412f5fbe9e958dcaded8c481237d95549a7e927c0c1ea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:27:24.000Z", "distro": "noble", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "36f230b24434ad2b04ebb89b97d24a0a0e3852be4f590056f571b9c9543e315f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T10:36:57.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "dedaa141e46403c5381bcf35aef22a01e9ad4fd68f44c07fc83b7154551fc617", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T10:37:45.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "90d218f7fafc0c940cf51f04602f471072ce564fc98667ebb289f8d02395e74c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-05-30T07:26:38.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "5d40dda1c3f5cfa7cec07390862d633a781cb0cbec7002eb7592e1de028e2a2b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:29:34.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "b8b6ffaa935c701a027c70b21835f9053fe4f40c0b27ca3275dbec3c48d00a14", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:30:42.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "fac3a474bf16a1f4c4772a73a8a6602db2b481da9a64e3b47d9da4f27897c20c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:25:13.000Z", "commit": "4fa1a918f85e2dd2ebebc1bbd452c84d2475b465", "fileid": "31cb73239f0b47c44471641a944b261097f902d4426fe6d52962876d1403a78b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677796813" } ] }