{ "_id": "6a1f472bb401979e73429ac7", "Package": "CONFESS", "Type": "Package", "Title": "Cell OrderiNg by FluorEScence Signal", "Version": "1.40.0", "Date": "2019-09-19", "Author": "Diana LOW and Efthimios MOTAKIS", "Maintainer": "Diana LOW ", "Description": "Single Cell Fluidigm Spot Detector.", "License": "GPL-2", "LazyData": "TRUE", "biocViews": "ImmunoOncology,\nGeneExpression,DataImport,CellBiology,Clustering,RNASeq,QualityControl,Visualization,TimeCourse,Regression,Classification", "Collate": "fluo_est.R fluo_NBE.R internal_fluo_NBE.R internal_fluo_est.R\ninternal_DDHF.R simulator.R cases.R", "RoxygenNote": "6.1.1", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Config/pak/sysreqs": "cmake libfftw3-dev libgdal-dev gdal-bin libgeos-dev\nmake libgsl0-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libssl-dev libproj-dev libsqlite3-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:43:14 UTC", "RemoteUrl": "https://github.com/bioc/CONFESS", "RemoteRef": "RELEASE_3_23", "RemoteSha": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "Packaged": { "Date": "2026-06-02 20:59:30 UTC", "User": "root" }, "MD5sum": "0a390d4e24fa7c8171a2dabec87256de", "_user": "bioc-release", "_type": "src", "_file": "CONFESS_1.40.0.tar.gz", "_fileid": "4f882f1cc2430c6fc67c2f3c3ece2b058c6b4407ef93a6ea65ba0204fdff7c8d", "_filesize": 3752957, "_sha256": "4f882f1cc2430c6fc67c2f3c3ece2b058c6b4407ef93a6ea65ba0204fdff7c8d", "_created": "2026-06-02T20:59:30.000Z", "_published": "2026-06-02T21:12:11.178Z", "_jobs": [ { "job": 79171730287, "time": 273, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7369792603" }, { "job": 79171730453, "time": 673, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7369929192" }, { "job": 79171730374, "time": 531, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7369879647" }, { "job": 79171730285, "time": 360, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7369822675" }, { "job": 79171730302, "time": 327, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7369811098" }, { "job": 79170335005, "time": 466, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7369693990" }, { "job": 79171730346, "time": 193, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7369764213" }, { "job": 79171730309, "time": 501, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7369870378" }, { "job": 79171730382, "time": 420, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7369843374" }, { "job": 79171730372, "time": 387, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7369831844" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CONFESS", "_commit": { "id": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "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": 1777380194 }, "_maintainer": { "name": "Diana LOW", "email": "lowdiana@gmail.com", "login": "dianalow", "description": "", "uuid": 3214561 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "grDevices", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "changepoint", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "contrast", "role": "Imports" }, { "package": "data.table", "version": ">= 1.9.7", "role": "Imports" }, { "package": "ecp", "role": "Imports" }, { "package": "EBImage", "role": "Imports" }, { "package": "flexmix", "role": "Imports" }, { "package": "flowCore", "role": "Imports" }, { "package": "flowClust", "role": "Imports" }, { "package": "flowMeans", "role": "Imports" }, { "package": "flowMerge", "role": "Imports" }, { "package": "flowPeaks", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "moments", "role": "Imports" }, { "package": "outliers", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "plotrix", "role": "Imports" }, { "package": "raster", "role": "Imports" }, { "package": "readbitmap", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "SamSPECTRAL", "role": "Imports" }, { "package": "waveslim", "role": "Imports" }, { "package": "wavethresh", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "CONFESSdata", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "geneexpression", "dataimport", "cellbiology", "clustering", "rnaseq", "qualitycontrol", "visualization", "timecourse", "regression", "classification" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 370, "source": "https://www.bioconductor.org/packages/stats/bioc/CONFESS" }, "_mentions": 2, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CONFESS.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "cluster2outlier", "createFluo", "defineLocClusters", "Fluo_adjustment", "Fluo_CV_modeling", "Fluo_CV_prep", "Fluo_inspection", "Fluo_modeling", "Fluo_ordering", "FluoSelection_byRun", "getFluo", "getFluo_byRun", "LocationMatrix", "pathEstimator", "readFiles", "simcells", "spotEstimator" ], "_datasets": [ { "name": "clu", "title": "clu", "object": "clu", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "estimates", "title": "estimates", "object": "estimates", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "estimates.2", "title": "estimates.2", "object": "estimates.2", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "files", "title": "files", "object": "files", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "Results", "title": "Results", "object": "Results", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step1", "title": "step1", "object": "step1", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step2", "title": "step2", "object": "step2", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step2.1", "title": "step2.1", "object": "step2.1", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step3", "title": "step3", "object": "step3", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step3.1", "title": "step3.1", "object": "step3.1", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "step4", "title": "step4", "object": "step4", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "steps2_4", "title": "steps2_4", "object": "steps2_4", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "clu", "title": "clu", "topics": [ "clu" ] }, { "page": "cluster2outlier", "title": "cluster2outlier", "topics": [ "cluster2outlier" ] }, { "page": "createFluo", "title": "createFluo", "topics": [ "createFluo" ] }, { "page": "defineLocClusters", "title": "defineLocClusters", "topics": [ "defineLocClusters" ] }, { "page": "estimates", "title": "estimates", "topics": [ "estimates" ] }, { "page": "estimates.2", "title": "estimates.2", "topics": [ "estimates.2" ] }, { "page": "files", "title": "files", "topics": [ "files" ] }, { "page": "Fluo_adjustment", "title": "Fluo_adjustment", "topics": [ "Fluo_adjustment" ] }, { "page": "Fluo_CV_modeling", "title": "Fluo_CV_modeling", "topics": [ "Fluo_CV_modeling" ] }, { "page": "Fluo_CV_prep", "title": "Fluo_CV_prep", "topics": [ "Fluo_CV_prep" ] }, { "page": "Fluo_inspection", "title": "Fluo_inspection", "topics": [ "Fluo_inspection" ] }, { "page": "Fluo_modeling", "title": "Fluo_modeling", "topics": [ "Fluo_modeling" ] }, { "page": "Fluo_ordering", "title": "Fluo_ordering", "topics": [ "Fluo_ordering" ] }, { "page": "FluoSelection_byRun", "title": "FluoSelection_byRun", "topics": [ "FluoSelection_byRun" ] }, { "page": "getFluo", "title": "getFluo", "topics": [ "getFluo" ] }, { "page": "getFluo_byRun", "title": "getFluo_byRun", "topics": [ "getFluo_byRun" ] }, { "page": "LocationMatrix", "title": "LocationMatrix", "topics": [ "LocationMatrix" ] }, { "page": "pathEstimator", "title": "pathEstimator", "topics": [ "pathEstimator" ] }, { "page": "readFiles", "title": "readFiles", "topics": [ "readFiles" ] }, { "page": "Results", "title": "Results", "topics": [ "Results" ] }, { "page": "simcells", "title": "simcells", "topics": [ "simcells" ] }, { "page": "spotEstimator", "title": "spotEstimator", "topics": [ "spotEstimator" ] }, { "page": "step1", "title": "step1", "topics": [ "step1" ] }, { "page": "step2", "title": "step2", "topics": [ "step2" ] }, { "page": "step2.1", "title": "step2.1", "topics": [ "step2.1" ] }, { "page": "step3", "title": "step3", "topics": [ "step3" ] }, { "page": "step3.1", "title": "step3.1", "topics": [ "step3.1" ] }, { "page": "step4", "title": "step4", "topics": [ "step4" ] }, { "page": "steps2_4", "title": "steps2_4", "topics": [ "steps2_4" ] } ], "_rundeps": [ "abind", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "biocmake", "bitops", "bmp", "bslib", "cachem", "changepoint", "checkmate", "cli", "cluster", "codetools", "colorspace", "contrast", "cpp11", "cytolib", "data.table", "DEoptimR", "digest", "dir.expiry", "EBImage", "ecp", "evaluate", "farver", "fastmap", "feature", "fftwtools", "filelock", "flexmix", "flowClust", "flowCore", "flowMeans", "flowMerge", "flowPeaks", "FNN", "fontawesome", "foreach", "foreign", "Formula", "fs", "generics", "ggplot2", "glue", "graph", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "isoband", "iterators", "jpeg", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "ks", "labeling", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "mclust", "memoise", "mgcv", "mime", "misc3d", "modeltools", "moments", "multcomp", "multicool", "multitaper", "mvtnorm", "nlme", "nnet", "outliers", "pcaPP", "plot3D", "plotrix", "plyr", "png", "polspline", "pracma", "quantreg", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "RCurl", "readbitmap", "reshape2", "Rgraphviz", "Rhdf5lib", "rlang", "rmarkdown", "rms", "robustbase", "rpart", "RProtoBufLib", "rrcov", "rstudioapi", "S4Vectors", "S7", "SamSPECTRAL", "sandwich", "sass", "scales", "snow", "sp", "SparseM", "statmod", "stringi", "stringr", "survival", "terra", "TH.data", "tiff", "tinytex", "vctrs", "viridisLite", "waveslim", "wavethresh", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "vignette_tex.Rnw", "filename": "vignette_tex.pdf", "title": "CONFESS", "engine": "knitr::knitr", "headings": [], "created": "2016-03-29 19:58:23", "modified": "2016-04-11 04:09:29", "commits": 2 }, { "source": "vignette.Rmd", "filename": "vignette.html", "title": "CONFESS", "author": "Diana LOW, Efthymios MOTAKIS", "engine": "knitr::rmarkdown", "headings": [ "Preliminaries", "Loading the packages", "Data pre-processing", "Fluorescence estimation", "Reading in image/text files", "Image spot estimation", "Quality control (identification of outliers)", "Re-estimation step (for outliers)", "Final estimation", "Fluorescence adjustment and estimation of cell cycle phases / pseudotime", "Fluorescence adjustment on estimations from Section 2.6", "Data inspection by batch (chip)", "If data consists of more than 1 chip run/batch", "If data consists of a single chip run/batch", "Cross-validation to assess the stability of the estimates" ], "created": "2016-03-29 19:58:23", "modified": "2019-02-26 01:51:47", "commits": 3 } ], "_score": 3.9030899869919438, "_indexed": false, "_nocasepkg": "confess", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/CONFESS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.40.0", "date": "2026-06-02T21:04:56.000Z", "distro": "noble", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "1c6099333aa5c7754e20eb9d017983af8365e5773bedf2a70ee52a04b11e6449", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.6.0", "os": "linux", "version": "1.40.0", "date": "2026-06-02T21:04:04.000Z", "distro": "noble", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "8fabb4b8a15e4bba6025cbdef2d795207d9855a23d7849fd5685ecd60f1665ec", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.5.3", "os": "mac", "version": "1.40.0", "date": "2026-06-02T21:02:31.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "98a54242817d3c980f17d0e05c3a8f85a0c28a46762d1a40a923a9c29d9c1d33", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.6.0", "os": "mac", "version": "1.40.0", "date": "2026-06-02T21:02:17.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "e74d2af1254e4b829fcfd7d77fcbac7f112431144d1c35efdc7d96fcb02a0fec", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.6.0", "os": "wasm", "version": "1.40.0", "date": "2026-06-02T21:03:37.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "7fe50c1f4e364ceb164a44590d2a0a00e450595c69a8ab1f378a33634a03dc27", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.7.0", "os": "win", "version": "1.40.0", "date": "2026-06-02T21:03:45.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "3cb558a53956a915f2e521ec83e2194e03aa71848ed548da86c087a9efb4e7db", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.5.3", "os": "win", "version": "1.40.0", "date": "2026-06-02T21:02:09.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "2be0cbbadde75236647031d3c53f7193427903e7f14f55b07890ca05d83f80b5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" }, { "r": "4.6.0", "os": "win", "version": "1.40.0", "date": "2026-06-02T21:02:12.000Z", "commit": "fe2e932367d1449a2e86901e53046c7ac3b8eeed", "fileid": "4a687c4e42b06fb4a5a22804f69d25e9e6584ab6cb1222827679e914489029aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26847339759" } ] }