{ "_id": "6abaa25199f7aa8c6aa420d6", "Package": "dawnn", "Title": "Differential Abundance with Neural Networks", "Version": "2.2.0", "Authors@R": "c(person(given = \"George\",\nfamily = \"Hall\",\nrole = c(\"aut\", \"cre\"),\nemail = \"george.hall@ucl.ac.uk\",\ncomment = c(ORCID = \"0000-0002-4828-0668\")),\nperson(given = \"Sergi\",\nfamily = \"Castellano\",\nrole = c(\"aut\"),\nemail = \"s.castellano@ucl.ac.uk\",\ncomment = c(ORCID = \"0000-0002-5819-4210\")),\nperson(given = \"University College London\",\nrole = c(\"cph\")))", "Description": "Detects regions of differential abundance in single-cell\ntranscriptomic data by applying a pre-trained neural network\nmodel to the labels of each cell's nearest neighbours. Tests\nfor both local and global differential abundance, controlling\nthe false discovery rate with the Benjamini-Yekutieli\nprocedure. The method is described in Hall and Castellano\n(2023) .", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://george-hall-ucl.github.io/dawnn/,\nhttps://github.com/george-hall-ucl/dawnn", "BugReports": "https://github.com/george-hall-ucl/dawnn/issues", "SystemRequirements": "Python (>= 3.9) with TensorFlow (>= 2.0), typically\ninstalled in a conda environment and selected via the\n'tf_conda_env' argument of run_dawnn(). See the package\ndocumentation for setup instructions.", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://george-hall-ucl.r-universe.dev", "Date/Publication": "2026-09-28 16:13:51 UTC", "RemoteUrl": "https://github.com/george-hall-ucl/dawnn", "RemoteRef": "HEAD", "RemoteSha": "e809d74546faf5c95664c07d030a07e51fae1921", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-28 16:33:19 UTC", "User": "root" }, "Author": "George Hall [aut, cre] (ORCID: ),\nSergi Castellano [aut] (ORCID: ),\nUniversity College London [cph]", "Maintainer": "George Hall ", "_user": "george-hall-ucl", "_type": "src", "_file": "dawnn_2.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/57f81f3831a13a622f61ba05f11fee91cc618ad0ade03149646de486f73cbe56", "_filesize": 844148, "_sha256": "57f81f3831a13a622f61ba05f11fee91cc618ad0ade03149646de486f73cbe56", "_expires": "2027-01-06T17:22:23.000Z", "_created": "2026-09-28T16:33:19.000Z", "_published": "2026-09-28T17:22:25.124Z", "_jobs": [ { "job": 109028595125, "time": 260, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10983873291" }, { "job": 109028595065, "time": 270, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10984280290" }, { "job": 109028594974, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10986260940" }, { "job": 109028595092, "time": 323, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10986815846" }, { "job": 109026741044, "time": 264, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10983643059" }, { "job": 109028595048, "time": 190, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10984073272" }, { "job": 109028595094, "time": 178, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10982974940" }, { "job": 109028595131, "time": 189, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10984012979" }, { "job": 109028595061, "time": 187, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10982824945" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988", "_status": "success", "_upstream": "https://github.com/george-hall-ucl/dawnn", "_commit": { "id": "e809d74546faf5c95664c07d030a07e51fae1921", "author": "george-hall-ucl ", "committer": "george-hall-ucl ", "message": "Merge branch 'dev'\n", "time": 1790612031 }, "_maintainer": { "name": "George Hall", "email": "george.hall@ucl.ac.uk", "login": "george-hall-ucl", "description": "Research fellow in genomics at UCL Great Ormond Street Institute of Child Health. Interested in computational methods for the study of rare diseases in children", "uuid": 77325372, "orcid": "0000-0002-4828-0668" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "keras", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.7", "role": "Suggests" }, { "package": "callr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "pkgload", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" } ], "_owner": "george-hall-ucl", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-46", "n": 4 }, { "week": "2026-29", "n": 30 }, { "week": "2026-30", "n": 16 }, { "week": "2026-32", "n": 1 }, { "week": "2026-40", "n": 1 } ], "_tags": [ { "name": "v1.2.0", "date": "2026-07-15" }, { "name": "v2.0.0", "date": "2026-07-16" }, { "name": "v2.1.0", "date": "2026-08-19" } ], "_stars": 2, "_contributors": [ { "user": "george-hall-ucl", "count": 303, "uuid": 77325372 } ], "_userbio": { "uuid": 77325372, "type": "user", "name": "George Hall", "followers": 12, "description": "Research fellow in genomics at UCL Great Ormond Street Institute of Child Health. Interested in computational methods for the study of rare diseases in children" }, "_downloads": { "count": 396, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dawnn" }, "_devurl": "https://github.com/george-hall-ucl/dawnn", "_pkgdown": "https://george-hall-ucl.github.io/dawnn/", "_searchresults": 11, "_gitlfs": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dawnn.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/george-hall-ucl/dawnn", "_realowner": "george-hall-ucl", "_cranurl": true, "_releases": [ { "version": "2.1.1", "date": "2026-09-08" }, { "version": "2.2.0", "date": "2026-09-08" } ], "_exports": [ "download_model", "run_dawnn" ], "_help": [ { "page": "download_model", "title": "Download the neural network model used by Dawnn.", "topics": [ "download_model" ] }, { "page": "run_dawnn", "title": "Identify which cells are in regions of differential abundance using Dawnn.", "topics": [ "run_dawnn" ] } ], "_pkglogo": "https://github.com/george-hall-ucl/dawnn/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/george-hall-ucl/dawnn/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "BH", "bitops", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "commonmark", "config", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "digest", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "fs", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "irlba", "isoband", "jquerylib", "jsonlite", "keras", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "processx", "progressr", "promises", "ps", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppTOML", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "rstudioapi", "Rtsne", "S7", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "sourcetools", "sp", "spam", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "survival", "sys", "tensor", "tensorflow", "tfautograph", "tfruns", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "uwot", "vctrs", "viridisLite", "whisker", "withr", "xfun", "xtable", "yaml", "zeallot", "zoo" ], "_vignettes": [ { "source": "dawnn.Rmd", "filename": "dawnn.html", "title": "Dawnn vignette", "author": "George T. Hall and Sergi Castellano", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Main workflow", "Required parameters", "Output", "Optional parameters", "Changing model location", "Downloading a model from another location", "SessionInfo" ], "created": "2023-03-30 11:19:18", "modified": "2026-09-28 16:13:51", "commits": 9 } ], "_score": 4.740362689494244, "_indexed": true, "_nocasepkg": "dawnn", "_universes": [ "george-hall-ucl" ], "_previous": "2.0.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.0", "date": "2026-09-28T16:36:39.000Z", "distro": "resolute", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/03c7c11d158c7b288672b632fea383fe52c35b0122d614636fc745b0015bfa94", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.6.1", "os": "linux", "version": "2.2.0", "date": "2026-09-28T16:36:42.000Z", "distro": "resolute", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/c4628f348738088096c3f3b5d41375d35a766f83edc2457a9227a2f6f975e085", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.5.3", "os": "mac", "version": "2.2.0", "date": "2026-09-28T17:17:56.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/9266a239bb19c07ca3eaef900d13734c8353504ef809a66107a3593f12361393", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.6.1", "os": "mac", "version": "2.2.0", "date": "2026-09-28T17:19:15.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/e3bd82a445d0a5ed57805a424bc8e1816909438cfda08cbfe23fd2ca5fe9fe6a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.0", "date": "2026-09-28T16:36:55.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/c651a15cd5c94137a1d65cfac062319a75e0dbaf0f915e4c7a7ef78bc9fb0812", "status": "success", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.7.0", "os": "win", "version": "2.2.0", "date": "2026-09-28T16:35:07.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/5b9a4303738b4e96c33e9de62ddbfb180cbf7b67d22d6fdf595495c8fc9c5da6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.5.3", "os": "win", "version": "2.2.0", "date": "2026-09-28T16:35:12.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/18ef0b17b4b14572f5b640f45c6bb5511065bac5201cfba89eb9297dad395fd7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" }, { "r": "4.6.1", "os": "win", "version": "2.2.0", "date": "2026-09-28T16:35:09.000Z", "commit": "e809d74546faf5c95664c07d030a07e51fae1921", "fileid": "https://r2.ropensci.org/c4b2e7b72b7f1eade8122ae9e072001703a85bb656a3d4c6c66b468a7fdc2407", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/george-hall-ucl/actions/runs/36451330988" } ] }