{ "_id": "6a555d85ff0138dec5d67e5a", "Package": "imageTCGAutils", "Title": "Utility functions for working with histopathology images", "Version": "1.1.5", "Authors@R": "c(\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\",\n\"aut\", c(ORCID = \"0000-0002-3242-0582\", affiliation =\n\"CUNY Graduate School of Public Health and Health Policy,\nNew York, NY USA\")),\nperson(\"Ilaria\", \"Billato\", , \"ilaria.billato@phd.unipd.it\",\nc(\"aut\", \"cre\"), c(ORCID = \"0000-0002-3335-3254\",\naffiliation = \"Department of Biology, University of Padova\")\n),\nperson(\"Eslam\", \"Abousamra\", role = \"ctb\", comment = c(\naffiliation = \"CUNY Graduate School of Public Health and Health Policy,\nNew York, NY USA\")\n))", "Description": "Utility functions for working with CONCH data, listing\nremote files. One function assigns HoverNet nuclei to\nProvGigaPath tiles with a scale factor to align coordinates.\nProvides internal utility functions for 'imageFeatureTCGA' and\nmost functions are not meant for end users.", "biocViews": "Software, WorkflowStep, Preprocessing", "License": "Artistic-2.0", "BugReports": "https://github.com/waldronlab/imageTCGAutils/issues", "URL": "https://github.com/waldronlab/imageTCGAutils", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Date": "2026-07-13", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-13 19:50:31 UTC", "RemoteUrl": "https://github.com/bioc/imageTCGAutils", "RemoteRef": "HEAD", "RemoteSha": "fbb892f622d2270a6f6f292d7f446a112af284df", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-13 21:42:41 UTC", "User": "root" }, "Author": "Marcel Ramos [aut] (ORCID: ,\naffiliation: CUNY Graduate School of Public Health and Health\nPolicy, New York, NY USA),\nIlaria Billato [aut, cre] (ORCID:\n, affiliation: Department of\nBiology, University of Padova),\nEslam Abousamra [ctb] (affiliation: CUNY Graduate School of Public\nHealth and Health Policy, New York, NY USA)", "Maintainer": "Ilaria Billato ", "_user": "bioc", "_type": "src", "_file": "imageTCGAutils_1.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/8d4f8f441e2561d36c4168aa5370f6af80282cfb60438b233e6bd6f18a927f22", "_filesize": 3174157, "_sha256": "8d4f8f441e2561d36c4168aa5370f6af80282cfb60438b233e6bd6f18a927f22", "_expires": "2026-10-21T21:49:54.000Z", "_created": "2026-07-13T21:42:41.000Z", "_published": "2026-07-13T21:49:57.009Z", "_bioccheck": { "error": 0, "warning": 1, "note": 3 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638", "_status": "success", "_upstream": "https://github.com/bioc/imageTCGAutils", "_commit": { "id": "fbb892f622d2270a6f6f292d7f446a112af284df", "author": "LiNk-NY ", "committer": "LiNk-NY ", "message": "version bump 1.1.5\n", "time": 1783972231 }, "_maintainer": { "name": "Ilaria Billato", "email": "ilaria.billato@phd.unipd.it", "orcid": "0000-0002-3335-3254" }, "_distro": "resolute", "_jobs": [ { "job": 86943058614, "time": 239, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8293775502" }, { "job": 86943058587, "time": 372, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8293827234" }, { "job": 86943058583, "time": 367, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8293825274" }, { "job": 86943058660, "time": 221, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8293767742" }, { "job": 86943058636, "time": 289, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8293795634" }, { "job": 86941610280, "time": 443, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8293685178" }, { "job": 86943058602, "time": 218, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8293767165" }, { "job": 86943058715, "time": 254, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8293782071" }, { "job": 86943058765, "time": 253, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8293781225" }, { "job": 86943058687, "time": 260, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8293783916" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "BiocBaseUtils", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "anndataR", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "imageFeatureTCGA", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "paws", "role": "Suggests" }, { "package": "rhdf5", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sfdep", "role": "Suggests" }, { "package": "spdep", "role": "Suggests" }, { "package": "SpatialFeatureExperiment", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "wk", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-50", "n": 8 }, { "week": "2025-51", "n": 6 }, { "week": "2026-07", "n": 21 }, { "week": "2026-09", "n": 22 }, { "week": "2026-10", "n": 7 }, { "week": "2026-11", "n": 11 }, { "week": "2026-12", "n": 9 }, { "week": "2026-13", "n": 1 }, { "week": "2026-16", "n": 13 }, { "week": "2026-18", "n": 2 }, { "week": "2026-21", "n": 1 }, { "week": "2026-24", "n": 7 }, { "week": "2026-26", "n": 5 }, { "week": "2026-28", "n": 5 }, { "week": "2026-29", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.4", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "software", "workflowstep", "preprocessing" ], "_stars": 0, "_contributors": [ { "user": "link-ny", "count": 95, "uuid": 4392950 }, { "user": "billila", "count": 23, "uuid": 78036851 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "eabousam", "count": 1, "uuid": 84752326 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 446, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 212, "source": "https://www.bioconductor.org/packages/stats/bioc/imageTCGAutils" }, "_devurl": "https://github.com/waldronlab/imagetcgautils", "_searchresults": 3, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/imageTCGAutils.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/waldronlab/imagetcgautils", "_realowner": "bioc", "_cranurl": false, "_exports": [ "importCONCH", "listHoverNet", "listProvGiga", "matchHoverNetToTiles" ], "_help": [ { "page": "importCONCH", "title": "Import CONCH as a SpatialFeatureExperiment", "topics": [ "importCONCH" ] }, { "page": "listFiles", "title": "List available HoVerNet and Prov-Giga-Path data for TCGA cancers", "topics": [ "listFiles", "listHoverNet", "listProvGiga" ] }, { "page": "matchHoverNetToTiles", "title": "Match HoverNet Nuclei to ProvGigaPath Tiles", "topics": [ "matchHoverNetToTiles" ] } ], "_readme": "https://github.com/bioc/imageTCGAutils/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "Rcpp", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "imageTCGAutils.Rmd", "filename": "imageTCGAutils.html", "title": "imageTCGAutils", "author": "Ilaria Billato, Eslam Abousamra", "engine": "knitr::rmarkdown", "headings": [ "imageTCGAutils", "Introduction", "Installation", "Loading packages", "Import Prov-GigaPath tile level embeddings", "Embedding PCA", "Spatial Patterns", "Adding HoverNet Nuclei Features", "Visualizing Hovernet nuclei vs tile coordinates to see that they do not match", "Scale factor between nuclei coordinates and tile coordinates", "Session Info", "References" ], "created": "2026-02-26 22:16:24", "modified": "2026-04-14 10:49:08", "commits": 6 } ], "_score": 5.352182518111363, "_indexed": true, "_nocasepkg": "imagetcgautils", "_universes": [ "bioc", "waldronlab" ], "_previous": "1.1.4", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-07-13T21:47:19.000Z", "distro": "resolute", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/89ea5eadc28a20ce192f8c6b36c8bf13678519f42443b201992600572de062ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.6.1", "os": "linux", "version": "1.1.5", "date": "2026-07-13T21:47:06.000Z", "distro": "resolute", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/94c4e276f6f0c97ef31599d77335ff77c45f0a662a72b5331e4472a362b32ede", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.5.3", "os": "mac", "version": "1.1.5", "date": "2026-07-13T21:44:38.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/db84f18063d2879b5a47fc07a41b8e8456355e5311081a47c3743538252c9014", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.6.1", "os": "mac", "version": "1.1.5", "date": "2026-07-13T21:45:33.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/785636e3dfc47ee153d8a8964309c0c2c10f9947e0fd890cd22db3ad4fb8260e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.5", "date": "2026-07-13T21:46:52.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/8fc4c3c15807e24bf33e11032cfb0aaa4d7c38b44f204641fd88eddee9435fc8", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-07-13T21:45:07.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/79e549d82f747239d3b45d2901001bf33859af911ce5f72e1f33c0f40acf7722", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.5.3", "os": "win", "version": "1.1.5", "date": "2026-07-13T21:44:47.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/ba28260ce152cc3e1a4ba1f3f6222848b148d08a958f28a651ed7abd70997cb9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" }, { "r": "4.6.1", "os": "win", "version": "1.1.5", "date": "2026-07-13T21:45:10.000Z", "commit": "fbb892f622d2270a6f6f292d7f446a112af284df", "fileid": "https://r2.ropensci.org/ffe6c391742058fabd0ffdc7825ebb6d897e50b739e035e08d90695fe1c157ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29286912638" } ] }