{
  "_id": "6ad9db2e021a938ed758ed74",
  "Package": "scFeatureFilter",
  "Type": "Package",
  "Title": "A correlation-based method for quality filtering of single-cell\nRNAseq data",
  "Version": "1.33.0",
  "Authors@R": "c(\nperson(\"Angeles\", \"Arzalluz-Luque\", email = \"angeles.arzalluz@gmail.com\", role = c(\"aut\")),\nperson(\"Guillaume\", \"Devailly\", email = \"gdevailly@hotmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8878-9357\")),\nperson(\"Anagha\", \"Joshi\", role = c(\"aut\")))",
  "Description": "An R implementation of the correlation-based method\ndeveloped in the Joshi laboratory to analyse and filter\nprocessed single-cell RNAseq data. It returns a filtered\nversion of the data containing only genes expression values\nunaffected by systematic noise.",
  "License": "MIT + file LICENSE",
  "LazyData": "TRUE",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, SingleCell, RNASeq, Preprocessing,\nGeneExpression",
  "URL": "https://bioconductor.org/packages/scFeatureFilter/",
  "BugReports": "https://github.com/gdevailly/scFeatureFilter/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:03 UTC",
  "RemoteUrl": "https://github.com/bioc/scFeatureFilter",
  "RemoteRef": "HEAD",
  "RemoteSha": "8951808c6256a6390a42a4c459a153ae26d8de7f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 09:01:27 UTC",
    "User": "root"
  },
  "Author": "Angeles Arzalluz-Luque [aut],\nGuillaume Devailly [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8878-9357>),\nAnagha Joshi [aut]",
  "Maintainer": "Guillaume Devailly <gdevailly@hotmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "scFeatureFilter_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/80df2b5c3145f1957d6f696d5fca857dfd7c88deffd9d05fbb7a63d3c53cf7f0",
  "_filesize": 4634826,
  "_sha256": "80df2b5c3145f1957d6f696d5fca857dfd7c88deffd9d05fbb7a63d3c53cf7f0",
  "_expires": "2027-01-30T09:45:16.000Z",
  "_created": "2026-10-22T09:01:27.000Z",
  "_published": "2026-10-22T09:45:18.463Z",
  "_upstream": "https://github.com/bioc/scFeatureFilter",
  "_status": "success",
  "_maintainer": {
    "name": "Guillaume Devailly",
    "email": "gdevailly@hotmail.com",
    "login": "gdevailly",
    "mastodon": "@G_Devailly@mamot.fr",
    "twitter": "@G_Devailly",
    "description": "Researcher at INRAE, Toulouse, France",
    "uuid": 3610678,
    "orcid": "0000-0001-8878-9357"
  },
  "_jobs": [
    {
      "job": 119735429769,
      "time": 163,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12413947909"
    },
    {
      "job": 119735429972,
      "time": 332,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12414352973"
    },
    {
      "job": 119735429642,
      "time": 296,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12414118052"
    },
    {
      "job": 119735429724,
      "time": 190,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": ""
    },
    {
      "job": 119735429806,
      "time": 179,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12413704156"
    },
    {
      "job": 119732016693,
      "time": 469,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12414207243"
    },
    {
      "job": 119735429836,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12413458335"
    },
    {
      "job": 119735429931,
      "time": 2589,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12415654926"
    },
    {
      "job": 119735429883,
      "time": 2496,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12416975456"
    },
    {
      "job": 119735429983,
      "time": 1675,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12415742325"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904",
  "_commit": {
    "id": "8951808c6256a6390a42a4c459a153ae26d8de7f",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380423
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 0.7.3",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.1.0",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "version": ">= 1.5",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 0.1.2",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 1.3.4",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "singlecell",
    "rnaseq",
    "preprocessing",
    "geneexpression"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "gdevailly",
      "count": 42,
      "uuid": 3610678
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 582,
    "source": "https://www.bioconductor.org/packages/stats/bioc/scFeatureFilter"
  },
  "_devurl": "https://github.com/gdevailly/scfeaturefilter",
  "_searchresults": 29,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/scFeatureFilter.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/gdevailly/scfeaturefilter",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bin_scdata",
    "calculate_cvs",
    "correlate_windows",
    "correlations_to_densities",
    "define_top_genes",
    "determine_bin_cutoff",
    "filter_expression_table",
    "get_mean_median",
    "plot_correlations_distributions",
    "plot_mean_variance",
    "plot_metric",
    "plot_top_window_autocor",
    "sc_feature_filter"
  ],
  "_datasets": [
    {
      "name": "scData_hESC",
      "title": "Expression data from 32 human embryonic stem cells",
      "object": "scData_hESC",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "tracking_id",
        "GSM922224_hESCpassage0_Cell4_0",
        "GSM922225_hESCpassage0_Cell5_0",
        "GSM922226_hESCpassage0_Cell6_0",
        "GSM922227_hESCpassage0_Cell7_0",
        "GSM922228_hESCpassage0_Cell8_0",
        "GSM922230_hESCpassage0_Cell10_0",
        "GSM922250_hESCpassage10_Cell1_0",
        "GSM922251_hESCpassage10_Cell2_0",
        "GSM922252_hESCpassage10_Cell3_0",
        "GSM922253_hESCpassage10_Cell4_0",
        "GSM922254_hESCpassage10_Cell5_0",
        "GSM922255_hESCpassage10_Cell6_0",
        "GSM922256_hESCpassage10_Cell7_0",
        "GSM922257_hESCpassage10_Cell8_0",
        "GSM922258_hESCpassage10_Cell9_0",
        "GSM922259_hESCpassage10_Cell10_0",
        "GSM922260_hESCpassage10_Cell11_0",
        "GSM922261_hESCpassage10_Cell12_0",
        "GSM922262_hESCpassage10_Cell13_0",
        "GSM922263_hESCpassage10_Cell14_0",
        "GSM922264_hESCpassage10_Cell15_0",
        "GSM922265_hESCpassage10_Cell16_0",
        "GSM922266_hESCpassage10_Cell17_0",
        "GSM922267_hESCpassage10_Cell18_0",
        "GSM922268_hESCpassage10_Cell19_0",
        "GSM922269_hESCpassage10_Cell20_0",
        "GSM922270_hESCpassage10_Cell21_0",
        "GSM922271_hESCpassage10_Cell22_0",
        "GSM922272_hESCpassage10_Cell23_0",
        "GSM922273_hESCpassage10_Cell24_0",
        "GSM922274_hESCpassage10_Cell25_0",
        "GSM922275_hESCpassage10_Cell26_0"
      ],
      "rows": 60468,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bin_scdata",
      "title": "Bin genes by mean expression.",
      "topics": [
        "bin_scdata"
      ]
    },
    {
      "page": "calculate_cvs",
      "title": "Compute mean expression level, standard deviation and coefficient of variation of each feature.",
      "topics": [
        "calculate_cvs"
      ]
    },
    {
      "page": "correlate_windows",
      "title": "Calculate correlations against top window.",
      "topics": [
        "correlate_windows"
      ]
    },
    {
      "page": "correlations_to_densities",
      "title": "Transform the correlation table to density distributions of correlation values",
      "topics": [
        "correlations_to_densities"
      ]
    },
    {
      "page": "define_top_genes",
      "title": "Define the reference window using the most highly expressed features.",
      "topics": [
        "define_top_genes"
      ]
    },
    {
      "page": "determine_bin_cutoff",
      "title": "Determine a threshold for selecting bins of features based on the metric table",
      "topics": [
        "determine_bin_cutoff"
      ]
    },
    {
      "page": "filter_expression_table",
      "title": "Filter binned expression matrix",
      "topics": [
        "filter_expression_table"
      ]
    },
    {
      "page": "get_mean_median",
      "title": "Extract mean and median correlation coefficient values",
      "topics": [
        "get_mean_median"
      ]
    },
    {
      "page": "plot_correlations_distributions",
      "title": "Produce a density plot of correlation values for each window of feature",
      "topics": [
        "plot_correlations_distributions"
      ]
    },
    {
      "page": "plot_mean_variance",
      "title": "Produce a mean expression x coefficient of variation scatter plot.",
      "topics": [
        "plot_mean_variance"
      ]
    },
    {
      "page": "plot_metric",
      "title": "Produce a bar chart of mean (or median) correlation coefficient per bin of feature.",
      "topics": [
        "plot_metric"
      ]
    },
    {
      "page": "plot_top_window_autocor",
      "title": "Utility plot to choose a top_window size",
      "topics": [
        "plot_top_window_autocor"
      ]
    },
    {
      "page": "sc_feature_filter",
      "title": "Filter scRNA-seq expression matrix to keep only highly informative features. Integrated pipeline.",
      "topics": [
        "sc_feature_filter"
      ]
    },
    {
      "page": "scData_hESC",
      "title": "Expression data from 32 human embryonic stem cells",
      "topics": [
        "scData_hESC"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scFeatureFilter/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "Introduction to the scFeatureFilter package",
      "author": "Angeles Arzalluz-Luque, Guillaume Devailly, Anagha Joshi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Preamble",
        "Package aim",
        "Method summary",
        "Installation",
        "Integrated usage",
        "Detailed usage",
        "Loading data",
        "Binning data",
        "Correlation of the bins",
        "Choosing a threshold",
        "Working with SingleCellExperiment objects",
        "Parameter values",
        "max_zeros",
        "top_window_size",
        "other_window_size",
        "n_random",
        "threshold"
      ],
      "created": "2017-09-26 15:03:05",
      "modified": "2026-02-23 16:53:46",
      "commits": 14
    }
  ],
  "_score": 5.337459261290656,
  "_indexed": true,
  "_nocasepkg": "scfeaturefilter",
  "_universes": [
    "bioc",
    "gdevailly"
  ],
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-09-22T08:55:28.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/88df700b1dc47aad480762754f36adda372fad4f103677caa6ca0c4a104c58e7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35706733268"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-10-22T09:06:10.000Z",
      "distro": "resolute",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/803e5b3ae266d3b8dd651882a50eaac6aa0e8b09fdb0236c4b6d8a9151f1c338",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-10-22T09:05:42.000Z",
      "distro": "resolute",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/0827227691f019b3628607c7d7b8ff8cd931844244e80abcbba5319a0a8292fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-10-22T09:03:48.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/111263b52ab3a4e27675c99915e984bc11e2ea638e9bdce52fd9cdd4aa92c260",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-10-22T09:04:11.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/50a80c8000f6940dc2739b3ef55e7be31be9ca7bb6a1b28c9925128e5737fe77",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-22T09:43:35.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/db724e9417286da3e81a24811636b557e34b4fac8ea844302d8d3af3d89b7ab7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-22T09:42:09.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/9e420cd95acd67003051b8c771dd55bd5e104c67a9cf0a8dcfe851e586e43be7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-10-22T09:28:19.000Z",
      "commit": "8951808c6256a6390a42a4c459a153ae26d8de7f",
      "fileid": "https://r2.ropensci.org/689619da673898e088c0136cbfb3a39be40cdfeb492031319477537a2e82d20e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39751187904"
    }
  ]
}