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"Phosphosite annotation", "topics": [ "siteAnnotate" ] }, { "page": "SPSs", "title": "A list of Stably 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/RELEASE_3_23/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", 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Di Xiao, Pengyi Yang", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading 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": 5.28330122870355, "_indexed": false, "_nocasepkg": "phosr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/PhosR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T07:41:23.000Z", "distro": "noble", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "41d1ba61aaa676246abcd1a23f9db6a5c1cb4ca99a83dcbc6f4285b69c31c223", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.6.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T07:42:02.000Z", "distro": "noble", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "79c416040131437c1a967b3033e1e8180a1e778d675490273726f5a2c1737f26", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.5.3", "os": "mac", "version": "1.22.0", "date": "2026-05-29T08:45:11.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "e647327f1d2d6debbd043e1964eda9984c0f32a5584e859dd7f0e25573b90131", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.6.0", "os": "mac", "version": "1.22.0", "date": "2026-05-29T08:45:45.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "55b7d5bdfe98b8c425d5f909058a66b9fd0650a27c763946973ffd3d7c390e86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.6.0", "os": "wasm", "version": "1.22.0", "date": "2026-05-29T07:41:38.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "1efe7af98f38a36a7dcd1d8c16a37ccbc262f02410535f70d241e633f148675f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.7.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:46:34.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "dc28147eb6aabd302a77dcbfe686cdcb25623028311c1c1b0fb353fe3ff597c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.5.3", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:45:48.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "d5ddfc3097ae2b0b5733f704bbab49370d3b767cf390a81684391c3fafcfcc34", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" }, { "r": "4.6.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:45:47.000Z", "commit": "5abc7acea28880d1d603bd55ad7e00fad5e9ef25", "fileid": "69c0a02b0cf286777df1c0bba7328e8a4de9abe487538e11fb0c8eeab6f80d5a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624372270" } ] }