{ "_id": "6acd6f90a14063b82c3ab804", "Package": "RPBC", "Title": "Region-Preserving Batch Correction for Paired Region-Resolved\nSingle-Cell Data", "Version": "0.99.0", "Authors@R": "person(\ngiven = \"Elizabeth B.\",\nfamily = \"Amona\",\nemail = \"amonaelizabeth1@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7575-788X\")\n)", "Description": "Implements Region-Preserving Batch Correction (RPBC), an\nempirical-Bayes location-scale framework for paired\nregion-resolved single-cell and spatial-omics data. RPBC\npreserves a patient-balanced population-average regional\ncontrast while harmonizing patient-wide location shifts,\npatient-specific regional deviations, and patient-region scale\nheterogeneity. The package also provides Adaptive RPBC for\ngroup-size-dependent stabilization of patient-region scale\nvariation and covariate-adjusted RPBC for preserving\nprespecified patient-level covariate-associated variation\nduring harmonization. RPBC is designed to interoperate with\nBioconductor data structures for single-cell and spatial\nexperiments.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.0", "biocViews": "BatchEffect, Preprocessing, SingleCell, Spatial,\nStatisticalMethod", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libssl-dev\nzlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-10-12 19:37:57 UTC", "RemoteUrl": "https://github.com/BiocStaging/RPBC", "RemoteRef": "HEAD", "RemoteSha": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 23:14:21 UTC", "User": "root" }, "Author": "Elizabeth B. Amona [aut, cre] (ORCID:\n)", "Maintainer": "Elizabeth B. Amona ", "_user": "biocstaging", "_type": "src", "_file": "RPBC_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/5bcc34a4f97fe8409fc9d5baa9e88bd8ca448d5bc5440fa539451089ed639b2e", "_filesize": 160528, "_sha256": "5bcc34a4f97fe8409fc9d5baa9e88bd8ca448d5bc5440fa539451089ed639b2e", "_expires": "2027-01-20T23:38:53.000Z", "_created": "2026-10-12T23:14:21.000Z", "_published": "2026-10-12T23:38:56.090Z", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_upstream": "https://github.com/BiocStaging/RPBC", "_commit": { "id": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "author": "Elizabeth B. Amona ", "committer": "Elizabeth B. Amona ", "message": "Remove local validation files from repository\n", "time": 1791833877 }, "_maintainer": { "name": "Elizabeth B. Amona", "email": "amonaelizabeth1@gmail.com", "login": "elizabethamona", "description": "", "uuid": 80857204, "orcid": "0000-0002-7575-788X" }, "_distro": "resolute", "_jobs": [ { "job": 115049222519, "time": 152, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11778109730" }, { "job": 115049222616, "time": 207, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11778968992" }, { "job": 115049222491, "time": 245, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11778384591" }, { "job": 115049222515, "time": 198, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11778559391" }, { "job": 115049222664, "time": 164, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11779497609" }, { "job": 115047810323, "time": 289, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11778647151" }, { "job": 115049222443, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11778858650" }, { "job": 115049222470, "time": 170, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11778309590" }, { "job": 115049222523, "time": 200, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11778607736" }, { "job": 115049222732, "time": 161, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11778664088" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "matrixStats", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SpatialExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-42", "n": 2 } ], "_tags": [], "_topics": [ "batcheffect", "preprocessing", "singlecell", "spatial", "statisticalmethod" ], "_stars": 0, "_contributors": [ { "user": "elizabethamona", "count": 2, "uuid": 80857204 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RPBC" }, "_devurl": "https://github.com/biocstaging/rpbc", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/RPBC.html", "LICENSE" ], "_cranurl": false, "_exports": [ "rpbc" ], "_datasets": [ { "name": "haley_gbm_example", "title": "Haley GBM IMC Example Dataset", "object": "haley_gbm_example", "file": "haley_gbm_example.rda", "class": [ "SpatialExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "haley_gbm_example", "title": "Haley GBM IMC Example Dataset", "topics": [ "haley_gbm_example" ] }, { "page": "rpbc", "title": "Region-Preserving Batch Correction", "topics": [ "rpbc" ] } ], "_rundeps": [ "abind", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "lattice", "lifecycle", "magick", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "openssl", "pillar", "pkgconfig", "purrr", "R6", "Rcpp", "rjson", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SpatialExperiment", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "RPBC.Rmd", "filename": "RPBC.html", "title": "RPBC: Region-Preserving Batch Correction", "author": "Elizabeth B. Amona, PhD", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Example dataset", "Input assay and transformation", "Ordinary RPBC", "Adaptive RPBC", "Covariate-adjusted RPBC", "Accessing harmonized values", "Choosing an RPBC workflow", "Additional fit information", "Session information" ], "created": "2026-10-12 18:19:21", "modified": "2026-10-12 18:19:21", "commits": 1 } ], "_score": 2, "_indexed": true, "_nocasepkg": "rpbc", "_universes": [ "biocstaging", "elizabethamona" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-10-12T23:18:33.000Z", "distro": "resolute", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/83b7c31433641da3bcffb3b2384c6134f9c59e9dda8c33ff6b8f787bb7cea1b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-10-12T23:18:34.000Z", "distro": "resolute", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/4a80527983cfd64eb6514d95a274e5cbe7cfc3cc97db3114583978c92e86e2af", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-10-12T23:32:31.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/3adfd030a7681a176b9f48ccc22b6f7b22ed01f8517de975b7e28e057ffbbfe4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-10-12T23:36:54.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/adfa0d83ffed3cf580eec0e042b7529d6ebf6a7f1f70ed2fc448618c4385e837", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-10-12T23:18:43.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/add0c29140a15e98a323e37de1a5cc2db73a2c8ad36ab06619a3bb7af4a18fcb", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-10-12T23:17:44.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/0ca883e0bfd1fc937a815a32e0ec236afaa1904356cbf068d7055be79f4a1f9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-10-12T23:17:31.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/b6f879564881054376d4f7c9ca6f64cfcb091775f3ef87d298516d1e63fd184d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-10-12T23:17:46.000Z", "commit": "8db3a51a4014c1fffe88f70994e83ab089ef9a40", "fileid": "https://r2.ropensci.org/3c6cf46c5dfe2529fe9cae67829b3f776651860971b090fcc34ad502b2d9cc97", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/38320662087" } ] }