{ "_id": "6ac790acde46216d5edd246d", "Package": "AlphaMissenseR", "Title": "Accessing AlphaMissense Data Resources in R", "Version": "1.8.1", "Authors@R": "c(person(\n\"Martin\", \"Morgan\", role = c(\"aut\", \"cre\"),\nemail = \"mtmorgan.xyz@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5874-8148\")\n), person(\n\"Tram\", \"Nguyen\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-4809-6227\")\n), person(\n\"Tyrone\", \"Lee\",\nrole = \"ctb\"\n), person(\n\"Nitesh\", \"Turaga\",\nrole = \"ctb\"\n), person(\n\"Chan Zuckerberg Initiative DAF CZF2019-002443\",\nrole = \"fnd\"\n), person(\n\"NIH NCI ITCR U24CA180996\",\nrole = \"fnd\"\n), person(\n\"NIH NCI IOTN U24CA232979\",\nrole = \"fnd\"\n), person(\n\"NIH NCI ARTNet U24CA274159\",\nrole = \"fnd\"\n))", "Description": "The AlphaMissense publication\n\noutlines how a variant of AlphaFold / DeepMind was used to\npredict missense variant pathogenicity. Supporting data on\nZenodo include, for\ninstance, 71M variants across hg19 and hg38 genome builds. The\n'AlphaMissenseR' package allows ready access to the data,\ndownloading individual files to DuckDB databases for\nexploration and integration into *R* and *Bioconductor*\nworkflows.", "License": "Artistic-2.0", "URL": "https://mtmorgan.github.io/AlphaMissenseR/", "BugReports": "https://github.com/mtmorgan/AlphaMissenseR/issues", "biocViews": "SNP, Annotation, FunctionalGenomics, StructuralPrediction,\nTranscriptomics, VariantAnnotation, GenePrediction,\nImmunoOncology", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libssl-dev xz-utils", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-09-07 22:58:01 UTC", "RemoteUrl": "https://github.com/bioc/AlphaMissenseR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 11:24:57 UTC", "User": "root" }, "Author": "Martin Morgan [aut, cre] (ORCID:\n),\nTram Nguyen [aut] (ORCID: ),\nTyrone Lee [ctb],\nNitesh Turaga [ctb],\nChan Zuckerberg Initiative DAF CZF2019-002443 [fnd],\nNIH NCI ITCR U24CA180996 [fnd],\nNIH NCI IOTN U24CA232979 [fnd],\nNIH NCI ARTNet U24CA274159 [fnd]", "Maintainer": "Martin Morgan ", "_user": "bioc-release", "_type": "src", "_file": "AlphaMissenseR_1.8.1.tar.gz", "_fileid": "https://r2.ropensci.org/41ac485391b2d65574f110000084fcf28726d4932b762dffd38bae2f58f8a4ea", "_filesize": 2214436, "_sha256": "41ac485391b2d65574f110000084fcf28726d4932b762dffd38bae2f58f8a4ea", "_expires": "2027-01-16T12:46:34.000Z", "_created": "2026-10-08T11:24:57.000Z", "_published": "2026-10-08T12:46:36.777Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_upstream": "https://github.com/bioc/AlphaMissenseR", "_commit": { "id": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "author": "Martin Morgan ", "committer": "Martin Morgan ", "message": "version bump\n", "time": 1788821881 }, "_maintainer": { "name": "Martin Morgan", "email": "mtmorgan.xyz@gmail.com", "login": "mtmorgan", "orcid": "0000-0002-5874-8148", "description": "", "uuid": 118552 }, "_distro": "resolute", "_jobs": [ { "job": 113286755638, "time": 181, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11546874206" }, { "job": 113286755709, "time": 1849, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11548718582" }, { "job": 113286755598, "time": 1365, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11547448530" }, { "job": 113286755643, "time": 2100, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "11551182997" }, { "job": 113286755611, "time": 1314, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "11550566849" }, { "job": 113277722074, "time": 1491, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11547343461" }, { "job": 113286755728, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11547268925" }, { "job": 113286755659, "time": 1508, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11548059080" }, { "job": 113286755796, "time": 1464, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "11547944061" }, { "job": 113286755604, "time": 1535, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "11547598875" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "dplyr", "role": "Depends" }, { "package": "rjsoncons", "version": ">= 1.0.1", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "duckdb", "version": ">= 1.3.1", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "spdl", "role": "Imports" }, { "package": "memoise", "role": "Imports" }, { "package": "BiocBaseUtils", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "whisker", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "Seqinfo", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "AnnotationHub", "role": "Suggests" }, { "package": "ExperimentHub", "role": "Suggests" }, { "package": "ensembldb", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "r3dmol", "role": "Suggests" }, { "package": "bio3d", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "shiny.gosling", "role": "Suggests" }, { "package": "ggdist", "role": "Suggests" }, { "package": "colorspace", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-41", "n": 3 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-48", "n": 2 }, { "week": "2026-18", "n": 1 }, { "week": "2026-37", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.8.1", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "snp", "annotation", "functionalgenomics", "structuralprediction", "transcriptomics", "variantannotation", "geneprediction", "immunooncology" ], "_stars": 13, "_contributors": [ { "user": "tram-nguyen-n", "count": 115, "uuid": 150388074 }, { "user": "mtmorgan", "count": 91, "uuid": 118552 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "nturaga", "count": 9, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 474, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 390, "source": "https://www.bioconductor.org/packages/stats/bioc/AlphaMissenseR" }, "_devurl": "https://github.com/mtmorgan/alphamissenser", "_pkgdown": "https://mtmorgan.github.io/AlphaMissenseR/", "_searchresults": 13, "_rbuild": "4.6.1", "_assets": [ "extra/AlphaMissenseR.html", "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" ], "_homeurl": "https://github.com/mtmorgan/alphamissenser", "_realowner": "bioc", "_cranurl": false, "_exports": [ "af_colorfunc_by_position", "af_prediction_view", "af_predictions", "ALPHAMISSENSE_RECORD", "am_aa_pathogenicity", "am_aa_pos", "am_available", "am_browse", "am_data", "clinvar_data", "clinvar_plot", "db_connect", "db_disconnect", "db_disconnect_all", "db_range_join", "db_tables", "db_temporary_table", "gosling_plot", "to_GPos" ], "_help": [ { "page": "AlphaFold", "title": "AlphaFold Protein Structure Retrieval and Display", "topics": [ "af_colorfunc_by_position", "af_predictions", "af_prediction_view" ] }, { "page": "AlphaMissense", "title": "Retrieve AlphaMissense Resources as DuckDB Databases", "topics": [ "ALPHAMISSENSE_RECORD", "am_available", "am_browse", "am_data" ] }, { "page": "am_aa", "title": "Common Amino Acid-level Transformations", "topics": [ "am_aa_pathogenicity", "am_aa_pos" ] }, { "page": "ClinVar", "title": "Integrate ClinVar Labels with AlphaMissense Pathogenicity Scores", "topics": [ "clinvar_data", "clinvar_plot" ] }, { "page": "db", "title": "Manipulate the Database of Missense Mutations", "topics": [ "db_connect", "db_disconnect", "db_disconnect_all", "db_range_join", "db_tables", "db_temporary_table" ] }, { "page": "Gosling", "title": "Plot a GPos or GRanges Object Using Shiny and Gosling", "topics": [ "gosling_plot" ] }, { "page": "GenomicRanges", "title": "Create GenomicRanges Objects from AlphaMissense Annotations", "topics": [ "to_GPos" ] } ], "_readme": "https://github.com/bioc/AlphaMissenseR/raw/RELEASE_3_23/README.md", "_rundeps": [ "askpass", "BiocBaseUtils", "BiocFileCache", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "dplyr", "duckdb", "farver", "fastmap", "filelock", "generics", "ggplot2", "glue", "gtable", "httr2", "isoband", "labeling", "lifecycle", "magrittr", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppSpdlog", "rjsoncons", "rlang", "RSQLite", "S7", "scales", "spdl", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "whisker", "withr" ], "_score": 5.307067950661299, "_indexed": false, "_nocasepkg": "alphamissenser", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/AlphaMissenseR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.1", "date": "2026-10-08T11:29:07.000Z", "distro": "resolute", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/12646d7bf96376afe986e96d4e4b75d00b6c2334992ba1a5ea1ebf0e364969d8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.6.1", "os": "linux", "version": "1.8.1", "date": "2026-10-08T11:28:34.000Z", "distro": "resolute", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/10b856dabc6f6d822f11861257772cbdc73bd253f11bda5f982971714f8fa1df", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.5.3", "os": "mac", "version": "1.8.1", "date": "2026-10-08T12:13:07.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/7f66b245bde0b85d69b40af473a521b7fc0f906b3d0bac2a7d9b53be3a9e9d1b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.6.1", "os": "mac", "version": "1.8.1", "date": "2026-10-08T12:12:33.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/354334223994bec21cee0a99298c34504f0992eb13f63a700bb24751efb5d01c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.1", "date": "2026-10-08T11:27:46.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/6010cd981d60a6b946ec20bc43abb4bac87be4e49dbdf37a38dff8af24c8c872", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.7.0", "os": "win", "version": "1.8.1", "date": "2026-10-08T11:26:49.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/ff541d35eeb3c52bab0115de745a72330123a1c3c785d8a53bb3fa0354152ef4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.5.3", "os": "win", "version": "1.8.1", "date": "2026-10-08T11:27:10.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/a7c16ef925d4fb810de58457d12080f6ded892cfe6ccc049b62c70e85f362e86", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" }, { "r": "4.6.1", "os": "win", "version": "1.8.1", "date": "2026-10-08T11:27:54.000Z", "commit": "f7321f3c05faa62dd1dde108e5ae6005d2738e90", "fileid": "https://r2.ropensci.org/a72007cbcace8727366185201c1e658da5b0ac3f03ad39ad4940e5debb957a55", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37767170669" } ] }