{ "_id": "6a1ba7671d7bb097a0a1375f", "Package": "locusviz", "Type": "Package", "Title": "Yet Another Locus Visualization Package in R", "Version": "0.3.0", "Author": "Masahiro Kanai", "Maintainer": "Masahiro Kanai ", "Description": "This package provides various functions to visualize GWAS\ndata for a locus of interest using ggplot2.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Remotes": [ "caleblareau/BuenColors" ], "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev make libharfbuzz-dev libbz2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://mkanai.r-universe.dev", "Date/Publication": "2026-05-31 00:49:19 UTC", "RemoteUrl": "https://github.com/mkanai/locusviz", "RemoteRef": "HEAD", "RemoteSha": "0652daff9ad3d4100d65d30e9183bb24ae3a92ec", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 03:02:22 UTC", "User": "root" }, "MD5sum": "73af0e786194a91e99d26efe33d5f7ba", "_user": "mkanai", "_type": "src", "_file": "locusviz_0.3.0.tar.gz", "_fileid": "d6ed640bcdf462aea80a9e128a51bd34f64c325bccf40cd09d0875e5b9203257", "_filesize": 41171163, "_sha256": "d6ed640bcdf462aea80a9e128a51bd34f64c325bccf40cd09d0875e5b9203257", "_created": "2026-05-31T03:02:22.000Z", "_published": "2026-05-31T03:13:42.958Z", "_distro": "noble", "_jobs": [ { "job": 78695599921, "time": 472, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7313352902" }, { "job": 78695599926, "time": 553, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7313361684" }, { "job": 78695599920, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7313329520" }, { "job": 78695599932, "time": 272, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7313331391" }, { "job": 78695255327, "time": 388, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7313302873" }, { "job": 78695599915, "time": 267, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7313330851" }, { "job": 78695599952, "time": 389, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7313343534" }, { "job": 78695599962, "time": 415, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7313346633" }, { "job": 78695599930, "time": 392, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7313343860" } ], "_buildurl": "https://github.com/r-universe/mkanai/actions/runs/26701587030", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mkanai/locusviz", "_commit": { "id": "0652daff9ad3d4100d65d30e9183bb24ae3a92ec", "author": "Masahiro Kanai ", "committer": "Masahiro Kanai ", "message": "Add GENCODE v39 hg38 gene models from gnomAD v4.1.1\n\nUpdate the hg38 gene annotation resources to GENCODE v39, matching the\ngene models used by gnomAD v4.1.1 (VEP v105). 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"page": "binom_ci", "title": "Binomial confidence interval", "topics": [ "binom_ci" ] }, { "page": "boot_ci", "title": "Bootstrap confidence interval", "topics": [ "boot_ci" ] }, { "page": "compute_distance_to_gene", "title": "Compute distance from reference position to genes", "topics": [ "compute_distance_to_gene" ] }, { "page": "compute_functional_enrichment", "title": "Compute functional enrichment of variants by PIP bins", "topics": [ "compute_functional_enrichment" ] }, { "page": "distinct_shades", "title": "Generate distinct shades of a base color", "topics": [ "distinct_shades" ] }, { "page": "gencode_txdb", "title": "Create a TxDb object from GENCODE annotations", "topics": [ "gencode_txdb" ] }, { "page": "get_chromosome_sizes", "title": "Get chromosome sizes and cumulative positions", "topics": [ "get_chromosome_sizes" ] }, { "page": "get_cs_color_mapping", "title": "Get color mapping for credible sets", "topics": [ "get_cs_color_mapping" ] }, { "page": "get_default_theme", "title": "Get default ggplot2 theme for locusviz plots", "topics": [ "get_default_theme" ] }, { "page": "get_global_position", "title": "Convert chromosomal position to global genomic position", "topics": [ "get_global_position" ] }, { "page": "get_gnomad_colors", "title": "Get gnomAD population colors", "topics": [ "get_gnomad_colors" ] }, { "page": "get_pfam_domains", "title": "Get Pfam domain annotations for a gene", "topics": [ "get_pfam_domains" ] }, { "page": "get_tss_gene_body", "title": "Extract TSS and gene body information from TxDb", "topics": [ "get_tss_gene_body" ] }, { "page": "highlight_vline", "title": "Add vertical highlight lines to a plot", "topics": [ "highlight_vline" ] }, { "page": "jitter_labels", "title": "Jitter labels to avoid overlapping", "topics": [ "jitter_labels" ] }, { "page": "liftover_variant", "title": "Liftover variant positions between genome builds", "topics": [ "liftover_variant" ] }, { "page": "load_txdb", "title": "Load transcript database for gene annotations", "topics": [ "load_txdb" ] }, { "page": "mean_ci", "title": "Mean confidence interval via bootstrap", "topics": [ "mean_ci" ] }, { "page": "median_ci", "title": "Median confidence interval via bootstrap", "topics": [ "median_ci" ] }, { "page": "na_and", "title": "NA-safe AND operation", "topics": [ "na_and" ] }, { "page": "na_or", "title": "NA-safe OR operation", "topics": [ "na_or" ] }, { "page": "normalize_rank", "title": "Normalize scores by rank with exponential decay", "topics": [ "normalize_rank" ] }, { "page": "or_else", "title": "Return first non-NA value", "topics": [ "or_else" ] }, { "page": "or_missing", "title": "Conditionally return value or NULL", "topics": [ "or_missing" ] }, { "page": "parse_variant", "title": "Parse variant string into components", "topics": [ "parse_variant" ] }, { "page": "plot_fm_panel", "title": "Create fine-mapping panel", "topics": [ "plot_fm_panel" ] }, { "page": "plot_gene_panel", "title": "Create gene track panel", "topics": [ "plot_gene_panel" ] }, { "page": "plot_gene_score_panel", "title": "Create gene score visualization panel", "topics": [ "plot_gene_score_panel" ] }, { "page": "plot_locuszoom", "title": "Create LocusZoom-style visualization", "topics": [ "plot_locuszoom" ] }, { "page": "plot_lollipop", "title": "Create lollipop plot for variant effects", "topics": [ "plot_lollipop" ] }, { "page": "plot_manhattan_panel", "title": "Create Manhattan plot panel", "topics": [ "plot_manhattan_panel" ] }, { "page": "plot_r2_panel", "title": "Create r² (linkage disequilibrium) panel", "topics": [ "plot_r2_panel" ] }, { "page": "plot_upset", "title": "Create UpSet plot for set intersections", "topics": [ "plot_upset" ] }, { "page": "plot_upset_bar", "title": "Plot UpSet bar panel", "topics": [ "plot_upset_bar" ] }, { "page": "plot_upset_matrix", "title": "Plot UpSet matrix panel", "topics": [ "plot_upset_matrix" ] }, { "page": "preprocess", "title": "Preprocess GWAS data for visualization", "topics": [ "preprocess" ] }, { "page": "scale_color_chromosome", "title": "Create chromosome color scale for Manhattan plots", "topics": [ "scale_color_chromosome" ] }, { "page": "scale_x_chromosome", "title": "Create chromosome x-axis scale for genome-wide plots", "topics": [ "scale_x_chromosome" ] }, { "page": "spearman_ci", "title": "Spearman correlation confidence interval", "topics": [ "spearman_ci" ] }, { "page": "stat_summary_irq", "title": "Summary statistic with interquartile range", "topics": [ "stat_summary_irq" ] }, { "page": "trans_loglog_p", "title": "Create log-log transformation for p-values", "topics": [ "trans_loglog_p" ] }, { "page": "tss_v19_hg19", "title": "TSS and gene body data for GENCODE v19 (hg19/GRCh37)", "topics": [ "tss_v19_hg19" ] }, { "page": "tss_v34_hg38", "title": "TSS and gene body data for GENCODE v34 (hg38/GRCh38)", "topics": [ "tss_v34_hg38" ] }, { "page": "tss_v39_hg38", "title": "TSS and gene body data for GENCODE v39 (hg38/GRCh38)", "topics": [ 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