{ "_id": "6a1b03ed1d7bb097a0a02024", "Package": "barcodetrackR", "Type": "Package", "Title": "Functions for Analyzing Cellular Barcoding Data", "Version": "1.20.0", "Date": "2021-02-18", "Authors@R": "c(person(c(\"Diego\", \"Alexander\"), \"Espinoza\", email = \"diego.espinoza@pennmedicine.upenn.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Ryland\", \"Mortlock\", email = \"ryland.mortlock@nih.gov\", role = c(\"aut\")))", "Description": "barcodetrackR is an R package developed for the analysis\nand visualization of clonal tracking data. Data required is\nsamples and tag abundances in matrix form. Usually from\ncellular barcoding experiments, integration site retrieval\nanalyses, or similar technologies.", "URL": "https://github.com/dunbarlabNIH/barcodetrackR", "License": "file LICENSE", "LazyData": "FALSE", "Encoding": "UTF-8", "biocViews": "Software, Visualization, Sequencing", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:55:32 UTC", "RemoteUrl": "https://github.com/bioc/barcodetrackR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:27:50 UTC", "User": "root" }, "Author": "Diego Alexander Espinoza [aut, cre],\nRyland Mortlock [aut]", "Maintainer": "Diego Alexander Espinoza ", "MD5sum": "91eabac0dc814352da7aabb596004584", "_user": "bioc-release", "_type": "src", "_file": "barcodetrackR_1.20.0.tar.gz", "_fileid": "84547bac384d47b373de242e36045485fd51676ccc9012d7523be6e95dc88ef3", "_filesize": 3631438, "_sha256": "84547bac384d47b373de242e36045485fd51676ccc9012d7523be6e95dc88ef3", "_created": "2026-05-30T10:27:50.000Z", "_published": "2026-05-30T15:36:13.216Z", "_jobs": [ { "job": 78642656269, "time": 181, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307653895" }, { "job": 78642656276, "time": 354, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307670780" }, { "job": 78642656280, "time": 306, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7307666070" }, { "job": 78642656275, "time": 203, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7309281554" }, { "job": 78642656274, "time": 364, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "" }, { "job": 78640691460, "time": 269, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307514372" }, { "job": 78642656277, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307648991" }, { "job": 78642656289, "time": 243, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7307658138" }, { "job": 78642656301, "time": 232, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7307657023" }, { "job": 78642656293, "time": 287, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7307661775" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/barcodetrackR", "_commit": { "id": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380932 }, "_maintainer": { "name": "Diego Alexander Espinoza", "email": "diego.espinoza@pennmedicine.upenn.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "cowplot", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggdendro", "role": "Imports" }, { "package": "ggridges", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "proxy", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "magick", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-11", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "software", "visualization", "sequencing" ], "_stars": 5, "_contributors": [ { "user": "ryland-mortlock", "count": 185, "uuid": 58830770 }, { "user": "diegoalexespi", "count": 133, "uuid": 13153411 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/barcodetrackR" }, "_devurl": "https://github.com/dunbarlabnih/barcodetrackr", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/barcodetrackR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "barcode_binary_heatmap", "barcode_ggheatmap", "barcode_ggheatmap_stat", "barcode_stat_test", "bias_histogram", "bias_lineplot", "bias_ridge_plot", "chord_diagram", "clonal_contribution", "clonal_count", "clonal_diversity", "cor_plot", "create_SE", "dist_plot", "estimate_barcode_threshold", "get_top_clones", "launchApp", "mds_plot", "rank_abundance_plot", "rank_abundance_stat_test", "scatter_plot", "stat_hist", "subset_SE", "threshold", "threshold_SE" ], "_datasets": [ { "name": "wu_subset", "title": "Small subset of Wu barcoding dataset", "object": "wu_subset", "file": "wu_subset.rda", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "barcode_binary_heatmap", "title": "Barcode Binary Heatmap", "topics": [ "barcode_binary_heatmap" ] }, { "page": "barcode_ggheatmap", "title": "barcode_ggheatmap", "topics": [ "barcode_ggheatmap" ] }, { "page": "barcode_ggheatmap_stat", "title": "Barcode Top Clone Heatmap", "topics": [ "barcode_ggheatmap_stat" ] }, { "page": "barcode_stat_test", "title": "Barcode Statistical Test", "topics": [ "barcode_stat_test" ] }, { "page": "bias_histogram", "title": "Bias histogram", "topics": [ "bias_histogram" ] }, { "page": "bias_lineplot", "title": "Bias line plot", "topics": [ "bias_lineplot" ] }, { "page": "bias_ridge_plot", "title": "Bias Ridge plot", "topics": [ "bias_ridge_plot" ] }, { "page": "build_index_html", "title": "Build html", "topics": [ "build_index_html" ] }, { "page": "chord_diagram", "title": "Barcode Chord Diagram", "topics": [ "chord_diagram" ] }, { "page": "clonal_contribution", "title": "Clonal contribution plot", "topics": [ "clonal_contribution" ] }, { "page": "clonal_count", "title": "Clonal count plot", "topics": [ "clonal_count" ] }, { "page": "clonal_diversity", "title": "Clonal diversity plot", "topics": [ "clonal_diversity" ] }, { "page": "cor_plot", "title": "Correlation Plot", "topics": [ "cor_plot" ] }, { "page": "create_SE", "title": "create_SE", "topics": [ "create_SE" ] }, { "page": "dist_plot", "title": "Pairwise Distance Plot", "topics": [ "dist_plot" ] }, { "page": "estimate_barcode_threshold", "title": "Estimate Barcode Threshold", "topics": [ "estimate_barcode_threshold" ] }, { "page": "get_top_clones", "title": "get_top_clones (helper function)", "topics": [ "get_top_clones" ] }, { "page": "launchApp", "title": "Launch Barcode App", "topics": [ "launchApp" ] }, { "page": "mds_plot", "title": "MDS Plot", "topics": [ "mds_plot" ] }, { "page": "rank_abundance_plot", "title": "Rank Abundance Plot", "topics": [ "rank_abundance_plot" ] }, { "page": "rank_abundance_stat_test", "title": "Rank Abundance Statistical Test", "topics": [ "rank_abundance_stat_test" ] }, { "page": "scatter_plot", "title": "Scatter Plot", "topics": [ "scatter_plot" ] }, { "page": "stat_hist", "title": "Stat histogram", "topics": [ "stat_hist" ] }, { "page": "subset_SE", "title": "subset_SE", "topics": [ "subset_SE" ] }, { "page": "threshold", "title": "Threshold", "topics": [ "threshold" ] }, { "page": "threshold_SE", "title": "Threshold SE", "topics": [ "threshold_SE" ] }, { "page": "wu_subset", "title": "Small subset of Wu barcoding dataset", "topics": [ "wu_subset" ] } ], "_readme": "https://github.com/bioc/barcodetrackR/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "base64enc", "Biobase", "BiocGenerics", "bslib", "cachem", "circlize", "cli", "cluster", "colorspace", "commonmark", "cowplot", "cpp11", "DelayedArray", "digest", "dplyr", "farver", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "ggdendro", "ggplot2", "ggridges", "GlobalOptions", "glue", "gridExtra", "gtable", "htmltools", "httpuv", "IRanges", "isoband", "jquerylib", "jsonlite", "labeling", "later", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "otel", "permute", "pillar", "pkgconfig", "plyr", "promises", "proxy", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shape", "shiny", "sourcetools", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "withr", "xtable", "XVector" ], "_vignettes": [ { "source": "Introduction_to_barcodetrackR.Rmd", "filename": "Introduction_to_barcodetrackR.html", "title": "barcodetrackR", "author": "Diego A. Espinoza & Ryland D. Mortlock", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Contributors", "Loading data", "Loading required packages", "Creating objects with create_SE", "Assays created by create_SE", "Thresholding barcoding data", "Shiny app", "Correlations", "scatter_plot", "cor_plot", "Distances and similarities", "dist_plot", "Clonal patterns", "barcode_ggheatmap", "barcode_ggheatmap_stat", "barcode_binary_heatmap", "clonal_contribution", "Clonal bias", "bias_histogram", "bias_ridge_plot", "bias_lineplot", "Clone counts", "clonal_count", "Diversity", "rank_abundance", "clonal_diversity", "mds_plot", "Chord diagram", "Session Info" ], "created": "2020-02-24 19:28:01", "modified": "2021-04-04 20:35:06", "commits": 56 } ], "_score": 3.8750612633917, "_indexed": false, "_nocasepkg": "barcodetrackr", "_universes": [ "bioc-release" ], "_binaries": [ { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-04-30T09:45:14.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "cf79484270e27ab9d099b0b0efa2ac253f1540dc2b4d783cb214b7cb13990166", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/25151723224" }, { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-30T10:52:55.000Z", "distro": "noble", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "25fcdc3402bf106dd6e70adbc6836119d07356df5bc4601e9c3a02389f8c4a28", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-05-30T10:52:17.000Z", "distro": "noble", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "66b892c238052beb8d7d20eaa95b8c8fb72f5b3b36b3e6535bf041b172113c46", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-05-30T15:31:48.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "e7f8f097a32d63b10f9182fbc2b1422fba728ec42d36690d3480fab4a8f61033", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-05-30T10:51:52.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "b71fad2a22165ff9915818588468c1ec815aefa56ed69a2f17a2b946d79ecd7f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-05-30T10:50:36.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "b6205702367ab5ce74b08ef1e4c5e65b25b7496cc79c4ddd19cb7d534cf9e649", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-05-30T10:50:32.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "b602456d9e2e50ebf1de5198c7a545d8fa3a9d363505c618a7c87a3ab1f6569f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-05-30T10:50:20.000Z", "commit": "0735f99f0deb7c6d3c9bbfb18dd9368c9020b19a", "fileid": "7f923d02896a2e7b3954cafdc80cc3f617f51c280063d3efbb433acbee48ceaf", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680384459" } ] }