{ "_id": "6a4995006d67900babdfd215", "Package": "HarmonizR", "Title": "Handles missing values and makes more data available", "Version": "1.11.0", "Authors@R": "c(person(given = \"Simon\",\nfamily = \"Schlumbohm\",\nrole = c(\"aut\", \"cre\"),\nemail = \"schlumbohm@hsu-hh.de\"),\nperson(given = \"Julia\",\nfamily = \"Neumann\",\nrole = \"aut\"),\nperson(given = \"Philipp\",\nfamily = \"Neumann\",\nrole = \"aut\"))", "Description": "An implementation, which takes input data and makes it\navailable for proper batch effect removal by ComBat or Limma.\nThe implementation appropriately handles missing values by\ndissecting the input matrix into smaller matrices with\nsufficient data to feed the ComBat or limma algorithm. The\nadjusted data is returned to the user as a rebuild matrix. The\nimplementation is meant to make as much data available as\npossible with minimal data loss.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "biocViews": "BatchEffect", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:14 UTC", "RemoteUrl": "https://github.com/bioc/HarmonizR", "RemoteRef": "HEAD", "RemoteSha": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 23:12:30 UTC", "User": "root" }, "Author": "Simon Schlumbohm [aut, cre],\nJulia Neumann [aut],\nPhilipp Neumann [aut]", "Maintainer": "Simon Schlumbohm ", "_user": "bioc", "_type": "src", "_file": "HarmonizR_1.11.0.tar.gz", "_fileid": "https://r2.ropensci.org/ffc7067cdfcc0eded0f359ef52799f68844247e2398c85927b0b7a4da30bde41", "_filesize": 163297, "_sha256": "ffc7067cdfcc0eded0f359ef52799f68844247e2398c85927b0b7a4da30bde41", "_expires": "2026-10-12T23:19:26.000Z", "_created": "2026-07-04T23:12:30.000Z", "_published": "2026-07-04T23:19:28.600Z", "_bioccheck": { "error": 1, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859", "_status": "success", "_upstream": "https://github.com/bioc/HarmonizR", "_commit": { "id": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381274 }, "_maintainer": { "name": "Simon Schlumbohm", "email": "schlumbohm@hsu-hh.de", "login": "simonschlumbohm", "description": "", "uuid": 78701285 }, "_distro": "resolute", "_jobs": [ { "job": 85174767919, "time": 176, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8086294479" }, { "job": 85174767931, "time": 247, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8086301917" }, { "job": 85174767924, "time": 225, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8086299832" }, { "job": 85174767937, "time": 100, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8086313167" }, { "job": 85174767941, "time": 123, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8086315612" }, { "job": 85174571465, "time": 209, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8086276488" }, { "job": 85174767942, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086293914" }, { "job": 85174767935, "time": 114, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8086288458" }, { "job": 85174767930, "time": 112, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8086288282" }, { "job": 85174767936, "time": 124, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8086289556" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "doParallel", "version": ">= 1.0.16", "role": "Imports" }, { "package": "foreach", "version": ">= 1.5.1", "role": "Imports" }, { "package": "janitor", "version": ">= 2.1.0", "role": "Imports" }, { "package": "plyr", "version": ">= 1.8.6", "role": "Imports" }, { "package": "sva", "version": ">= 3.36.0", "role": "Imports" }, { "package": "seriation", "version": ">= 1.3.5", "role": "Imports" }, { "package": "limma", "version": ">= 3.46.0", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.11.0", "bioc": "3.24" }, { "branch": "release", "version": "1.10.0", "bioc": "3.23" } ], "_topics": [ "batcheffect" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 30, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HarmonizR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "harmonizR" ], "_help": [ { "page": "binary_matrix_reduction", "title": "Creating a binary existence matrix", "topics": [ "binary_matrix_reduction" ] }, { "page": "blocking", "title": "Blocking", "topics": [ "blocking" ] }, { "page": "build_key_list", "title": "Creation of keys", "topics": [ "build_key_list" ] }, { "page": "fetch_batch_overview", "title": "Fetching batch list", "topics": [ "fetch_batch_overview" ] }, { "page": "find_na", "title": "Finding NAs for the sorting process", "topics": [ "find_na" ] }, { "page": "format_from_S4", "title": "Format data taken from S4", "topics": [ "format_from_S4" ] }, { "page": "format_to_s4", "title": "Format data taken from HarmonizR back to S4", "topics": [ "format_to_s4" ] }, { "page": "harmonizR", "title": "Main function", "topics": [ "harmonizR" ] }, { "page": "jaccard", "title": "Jaccard-based sorting", "topics": [ "jaccard" ] }, { "page": "jaccard_index_absence", "title": "Jaccard index on zeroes (absence)", "topics": [ "jaccard_index_absence" ] }, { "page": "jaccard_index_existence", "title": "Jaccard index on ones (existence)", "topics": [ "jaccard_index_existence" ] }, { "page": "read_description", "title": "Reading description", "topics": [ "read_description" ] }, { "page": "read_main_data", "title": "Reading main data", "topics": [ "read_main_data" ] }, { "page": "rebuild", "title": "Rebuilding", "topics": [ "rebuild" ] }, { "page": "sorting", "title": "Sorting the input data.frame", "topics": [ "sorting" ] }, { "page": "splitting", "title": "Splitting", "topics": [ "splitting" ] }, { "page": "spotting_missing_values", "title": "Spotting", "topics": [ "spotting_missing_values" ] }, { "page": "unique_removal", "title": "Remove unique combinations", "topics": [ "unique_removal" ] }, { "page": "visual", "title": "Visualize feature means", "topics": [ "visual" ] }, { "page": "visual2", "title": "Visualize sample means", "topics": [ "visual2" ] }, { "page": "visual3", "title": "Visualize CV", "topics": [ "visual3" ] } ], "_readme": "https://github.com/bioc/HarmonizR/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "ca", "cachem", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "doParallel", "dplyr", "edgeR", "fastmap", "foreach", "formatR", "futile.logger", "futile.options", "gclus", "genefilter", "generics", "GenomicRanges", "glue", "hms", "httr", "IRanges", "iterators", "janitor", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "permute", "pillar", "pkgconfig", "plyr", "png", "purrr", "qap", "R6", "Rcpp", "registry", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "seriation", "snakecase", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "tibble", "tidyr", "tidyselect", "timechange", "TSP", "utf8", "vctrs", "vegan", "withr", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "HarmonizR_Vignette.Rmd", "filename": "HarmonizR_Vignette.html", "title": "HarmonizR_Vignette", "author": "Simon Schlumbohm", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Example Usage", "Parameters", "Session Information" ], "created": "2023-05-11 11:26:48", "modified": "2023-06-02 11:42:02", "commits": 2 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "harmonizr", "_universes": [ "bioc", "simonschlumbohm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-07-04T23:16:20.000Z", "distro": "resolute", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/d6ec6a81f7196a09966a7448ea00b7ef3496ac9ccaf9c9780723d73913bdda81", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.6.1", "os": "linux", "version": "1.11.0", "date": "2026-07-04T23:15:56.000Z", "distro": "resolute", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/7bcd8969ce80a04558921572fedffdd1a07adea4b0ee4d7cc2c3b6cb2ca85525", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-07-04T23:18:20.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/2ae654a39bc803597ec19aaafc0ab2bb299ab89f83f7ddaafcd12e9f5b318c78", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.6.1", "os": "mac", "version": "1.11.0", "date": "2026-07-04T23:18:41.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/369c7a7f35274ec1750df29e68e177fd7ade6d1a9a656da37789dfaf55ede5eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.6.0", "os": "wasm", "version": "1.11.0", "date": "2026-07-04T23:15:30.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/490208db4a5f10c16a9ef6262f220c529f62c84beaffad8d7fec3a99431d56ef", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.7.0", "os": "win", "version": "1.11.0", "date": "2026-07-04T23:13:57.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/af887df2405c722eedf52a2ebae0649993cec03570e624fc06f8732ffd6893cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.5.3", "os": "win", "version": "1.11.0", "date": "2026-07-04T23:13:53.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/b85af1decd17764ed2d773f886297adc379c09f21664e81ce2d7851c6393d77d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" }, { "r": "4.6.1", "os": "win", "version": "1.11.0", "date": "2026-07-04T23:14:06.000Z", "commit": "c6ddbb0a1669705dc8b4565981ed0849a6a4ebbb", "fileid": "https://r2.ropensci.org/5f86b437620e9db817bc8ad79d6867f8e43e37af3b602663f0fe52a54ac5699e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722620859" } ] }