{ "_id": "6ab378a43d719c1f8408fbd5", "Type": "Package", "Package": "scDiagnostics", "Title": "Cell type annotation diagnostics", "Version": "1.7.15", "Authors@R": "c(\nperson(\"Anthony\", \"Christidis\", role = c(\"aut\", \"cre\"),\nemail = \"anthony-alexander_christidis@hms.harvard.edu\",\ncomment = c(ORCID = \"0000-0002-4565-6279\")),\nperson(\"Andrew\", \"Ghazi\", role = \"aut\"),\nperson(\"Smriti\", \"Chawla\", role = \"aut\"),\nperson(\"Nitesh\", \"Turaga\", role = \"ctb\"),\nperson(\"Ludwig\", \"Geistlinger\", role = \"aut\"),\nperson(\"Robert\", \"Gentleman\", role = \"aut\")\n)", "Description": "The scDiagnostics package provides diagnostic plots to\nassess the quality of cell type assignments from single cell\ngene expression profiles. The implemented functionality allows\nto assess the reliability of cell type annotations, investigate\ngene expression patterns, and explore relationships between\ndifferent cell types in query and reference datasets allowing\nusers to detect potential misalignments between reference and\nquery datasets. The package also provides visualization\ncapabilities for diagnostics purposes.", "License": "Artistic-2.0", "URL": "https://github.com/ccb-hms/scDiagnostics,\nhttps://ccb-hms.github.io/scDiagnostics", "BugReports": "https://github.com/ccb-hms/scDiagnostics/issues", "VignetteBuilder": "knitr", "biocViews": "Annotation, Classification, Clustering, GeneExpression,\nRNASeq, SingleCell, Software, Transcriptomics", "Encoding": "UTF-8", "LazyDataCompression": "xz", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "LazyData": "true", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-23 01:24:22 UTC", "RemoteUrl": "https://github.com/bioc/scDiagnostics", "RemoteRef": "HEAD", "RemoteSha": "bee3ff588074c8e26c3b15b12610f23b7c19acdc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-23 06:14:50 UTC", "User": "root" }, "Author": "Anthony Christidis [aut, cre] (ORCID:\n),\nAndrew Ghazi [aut],\nSmriti Chawla [aut],\nNitesh Turaga [ctb],\nLudwig Geistlinger [aut],\nRobert Gentleman [aut]", "Maintainer": "Anthony Christidis ", "_user": "bioc", "_type": "src", "_file": "scDiagnostics_1.7.15.tar.gz", "_fileid": "https://r2.ropensci.org/4727cda7c37797aef73809dfb5eb555c60c0c3cb855050e814aeed98ca99106b", "_filesize": 8532217, "_sha256": "4727cda7c37797aef73809dfb5eb555c60c0c3cb855050e814aeed98ca99106b", "_expires": "2027-01-01T06:58:42.000Z", "_created": "2026-09-23T06:14:50.000Z", "_published": "2026-09-23T06:58:44.258Z", "_bioccheck": { "error": 0, "warning": 1, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35825403522", "_status": "success", "_upstream": "https://github.com/bioc/scDiagnostics", "_commit": { "id": "bee3ff588074c8e26c3b15b12610f23b7c19acdc", "author": "Anthony Christidis ", "committer": "Anthony Christidis ", "message": "Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15\n\nTwo failures on the first run against Bioconductor 3.24 / R 4.6:\n\nR CMD check reported significant warnings in the examples on all three\nplatforms. scran 1.41 deprecates its HVG helpers in favour of scrapper,\nso every modelGeneVar()/getTopHVGs() call - including the fitTrendVar()\nthat modelGeneVar() calls internally - now signals a deprecatedWarning,\nand rcmdcheck runs with error_on = \"warning\". Add an internal\nmuffleDeprecation() that muffles only the deprecatedWarning class,\nleaving genuine warnings alone, and wrap the six calls in processPCA(),\ndetectAnomaly() and calculateReconstructionError() with it. The three\nexamples that call scran::getTopHVGs() directly wrap it in\nsuppressWarnings() instead, with a comment saying why.\n\nThis is a stopgap: the HVG selection needs to move to scrapper before\nscran makes these functions defunct.\n\nThe macOS job additionally failed with \"Packages suggested but not\navailable: 'scRNAseq', 'celldex'\". 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