{ "_id": "6a1ee324b401979e73410e54", "Package": "CpmERCCutoff", "Type": "Package", "Title": "Calculation of Log2 Counts per Million Cutoff from ERCC Controls", "Version": "1.0.0", "Authors@R": "c(person(\"Tyler\", \"Grimes\", role = \"aut\", comment = c(ORCID = \"0000-0002-5653-3418\")), \nperson(c(\"Travis\", \"L.\"), \"Jensen\", role = \"aut\", comment = c(ORCID = \"0000-0002-0322-0469\")),\nperson(\"Kristen\", \"Steenbergen\", role = c(\"ctb\", \"cre\"), email = \"ksteenbergen@emmes.com\"),\nperson(\"The Emmes Company LLC\", role = \"cph\", comment = \"Copyright holder of CpmERCCutoff package (Copyright (C) 2022)\"),\nperson(c(\"Johannes\", \"B.\"), \"Goll\", role = \"aut\", comment = c(ORCID = \"0000-0002-9968-4080\")))", "Description": "Implementation of the empirical method to derive log2\ncounts per million (CPM) cutoff to filter out lowly expressed\ngenes using ERCC spike-ins as described in Goll and Bosinger\net.al (2022). This package\nutilizes the synthetic mRNA control pairs developed by the\nExternal RNA Controls Consortium (ERCC) (ERCC 1 / ERCC 2) that\nare spiked into sample pairs at known ratios at various\nabsolute abundances. The relationship between the observed and\nexpected fold changes is then used to empirically determine an\noptimal log2 CPM cutoff for filtering out lowly expressed\ngenes.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "Config/testthat/edition": "3", "RoxygenNote": "7.2.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 06:33:31 UTC", "User": "root" }, "Language": "en-US", "Author": "Tyler Grimes [aut] (),\nTravis L. Jensen [aut]\n(), Kristen Steenbergen\n[ctb, cre], The Emmes Company LLC [cph] (Copyright holder of\nCpmERCCutoff package (Copyright (C) 2022)), Johannes B. Goll\n[aut] ()", "Maintainer": "Kristen Steenbergen ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-09-13 10:20:07 UTC", "RemoteUrl": "https://github.com/cran/CpmERCCutoff", "RemoteRef": "HEAD", "RemoteSha": "53baa9c14369aa0af74d4e8eca7352619bc4ce2c", "MD5sum": "3a70d4ff2deb897e794edfd2c0792eb6", "_user": "cran", "_type": "src", "_file": "CpmERCCutoff_1.0.0.tar.gz", "_fileid": "79dd2f9390b37d4bcc70532874938aeb1db3fe120c68f34c581d0ad8faadaeea", "_filesize": 168416, "_sha256": "79dd2f9390b37d4bcc70532874938aeb1db3fe120c68f34c581d0ad8faadaeea", "_created": "2026-05-20T06:33:31.000Z", "_published": "2026-06-02T14:05:24.106Z", "_distro": "noble", "_jobs": [ { "job": 79089557683, "time": 116, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7102899260" }, { "job": 79089558125, "time": 116, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7102899332" }, { "job": 79089557342, "time": 177, "config": "source", "r": 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log2 CPM cutoff based on ERCC RNA spike-in", "topics": [ "getLowLcpmCutoff" ] }, { "page": "mta_dta", "title": "A data frame containing sample-level ERCC meta data", "topics": [ "mta_dta" ] }, { "page": "obs_input", "title": "A data frame of observed spike in ERCC normalized LCPM data", "topics": [ "obs_input" ] }, { "page": "plot.empLCPM", "title": "Plot the empirically derived LCPM cutoff", "topics": [ "plot.empLCPM" ] }, { "page": "print.empLCPM", "title": "Print the empirically derived LCPM cutoff results", "topics": [ "print.empLCPM" ] }, { "page": "summary.empLCPM", "title": "Summarizing the empirically derived LCPM cutoff", "topics": [ "summary.empLCPM" ] } ], "_rundeps": [], "_score": 1, "_indexed": true, "_nocasepkg": "cpmerccutoff", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-20T06:35:32.000Z", "distro": "noble", "commit": "53baa9c14369aa0af74d4e8eca7352619bc4ce2c", "fileid": 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