{ "_id": "6a1fa0e6b401979e7343219e", "Package": "ggDNAvis", "Title": "'ggplot2'-Based Tools for Visualising DNA Sequences and\nModifications", "Version": "1.0.0.9001", "Authors@R": "person(\n\"Evelyn\", \"Jade\",\nemail = \"evelynjade42@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0009-0003-7761-5425\")\n)", "Description": "Uses 'ggplot2' to visualise either (a) a single DNA/RNA\nsequence split across multiple lines, (b) multiple DNA/RNA\nsequences, each occupying a whole line, or (c) base\nmodifications such as DNA methylation called by modified bases\nmodels in Dorado or Guppy. Functions starting with\nvisualise_<>() are the main plotting functions, and functions\nstarting with extract_and_sort_<>() are key helper functions\nfor reading files and reformatting data. Source code is\navailable at , a full\nnon-expert user guide is available at\n, and an interactive\nweb-app version of the software is available at\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "LazyData": "true", "Language": "en-GB", "URL": "https://ejade42.github.io/ggDNAvis/,\nhttps://github.com/ejade42/ggDNAvis,\nhttps://doi.org/10.64898/2026.03.02.708895", "BugReports": "https://github.com/ejade42/ggDNAvis/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libfribidi-dev\nlibharfbuzz-dev libmagick++-dev gsfonts libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libwebp-dev libssl-dev", "Repository": "https://ejade42.r-universe.dev", "Date/Publication": "2026-06-03 02:59:03 UTC", "RemoteUrl": "https://github.com/ejade42/ggdnavis", "RemoteRef": "HEAD", "RemoteSha": "07a8671f48c1248589c5878e28564d2aa17b5a68", "NeedsCompilation": "no", 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visualisations", "object": "sequence_color_palettes", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "sequence_colour_palettes", "title": "Colour palettes for sequence visualisations", "object": "sequence_colour_palettes", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "bad_arg", "title": "Emit an error message for an invalid function argument (generic 'ggDNAvis' helper)", "topics": [ "bad_arg" ] }, { "page": "convert_base_to_number", "title": "Map a single base to the corresponding number (generic 'ggDNAvis' helper)", "topics": [ "convert_base_to_number" ] }, { "page": "convert_locations_to_MM_vector", "title": "Convert absolute index locations to MM tag ('write_modified_fastq()' helper)", "topics": [ "convert_locations_to_MM_vector" ] }, { "page": "convert_MM_vector_to_locations", "title": "Convert MM tag to absolute index locations (deprecated helper)", "topics": [ "convert_MM_vector_to_locations" ] }, { "page": "convert_modification_to_number_vector", "title": "Convert string-ified modification probabilities and locations to a single vector of probabilities ('visualise_methylation()' helper)", "topics": [ "convert_modification_to_number_vector" ] }, { "page": "convert_sequence_to_numbers", "title": "Map a sequence to a vector of numbers (generic 'ggDNAvis' helper)", "topics": [ "convert_sequence_to_numbers" ] }, { "page": "convert_sequences_to_matrix", "title": "Convert vector of sequences to character matrix (generic 'ggDNAvis' helper)", "topics": [ "convert_sequences_to_matrix" ] }, { "page": "create_image_data", "title": "Rasterise a vector of sequences into a numerical dataframe for ggplotting (generic 'ggDNAvis' helper)", "topics": [ "create_image_data" ] }, { "page": "debug_join_vector_num", "title": "Print a numeric vector to console ('ggDNAvis' debug helper)", "topics": [ "debug_join_vector_num" ] }, { "page": "debug_join_vector_str", "title": "Print a character/string vector to console ('ggDNAvis' debug helper)", "topics": [ "debug_join_vector_str" ] }, { "page": "example_many_sequences", "title": "Example multiple sequences data", "topics": [ "example_many_sequences" ] }, { "page": "extract_and_sort_methylation", "title": "Extract methylation information from dataframe for visualisation", "topics": [ "extract_and_sort_methylation", "extract_methylation_from_dataframe" ] }, { "page": "extract_and_sort_sequences", "title": "Extract, sort, and add spacers between sequences in a dataframe", "topics": [ "extract_and_sort_sequences", "extract_sequences_from_dataframe" ] }, { "page": "fastq_quality_scores", "title": "Vector of the quality scores used by the FASTQ format", "topics": [ "fastq_quality_scores" ] }, { "page": "format_time_diff", "title": "Format a difference between times (generic 'ggDNAvis' helper)", "topics": [ "format_time_diff" ] }, { "page": "ggDNAvis_aliases", "title": "'ggDNAvis' aliases", "topics": [ "aliases", "ggDNAvis_aliases" ] }, { "page": "ggDNAvis_shinyapp", "title": "Run the interactive 'ggDNAvis' shinyapp", "topics": [ "ggDNAvis_shiny", "ggDNAvis_shinyapp" ] }, { "page": "insert_at_indices", "title": "Insert blank items at specified indices in a vector ('visualise_many_sequences()' helper)", "topics": [ "insert_at_indices" ] }, { "page": "merge_fastq_with_metadata", "title": "Merge FASTQ data with metadata", "topics": [ "merge_fastq_with_metadata" ] }, { "page": "merge_methylation_with_metadata", "title": "Merge methylation with metadata", "topics": [ "merge_methylation_with_metadata" ] }, { "page": "monitor", "title": "Continue performance monitoring (generic 'ggDNAvis' helper)", "topics": [ "monitor" ] }, { "page": "monitor_start", "title": "Start performance monitoring (generic 'ggDNAvis' helper)", "topics": [ "monitor_start" ] }, { "page": "rasterise_index_annotations", "title": "Process index annotations and rasterise to a x/y/layer dataframe (generic 'ggDNAvis' helper)", "topics": [ 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