{ "_id": "6a20018ab401979e73445bfa", "Package": "Rgff", "Title": "R Utilities for GFF Files", "Version": "0.1.7", "Authors@R": "c(\nperson(\"Juan Antonio\", \"Garcia-Martin\", email = \"ja.garcia@cnb.csic.es\", role = c(\"cre\",\"aut\"),\ncomment = c(ORCID = \"0000-0003-0993-4064\")),\nperson(\"Juan Carlos\", \"Oliveros\", email = \"oliveros@cnb.csic.es\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-4520-0853\")),\nperson(\"Rafael\", \"Torres-Perez\", email = \"rafael.torres@cnb.csic.es\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-3696-4720\")))", "Author": "Juan Antonio Garcia-Martin [cre, aut] (ORCID:\n), Juan Carlos Oliveros\n[aut, ctb] (ORCID: ),\nRafael Torres-Perez [aut, ctb] (ORCID:\n)", "Maintainer": "Juan Antonio Garcia-Martin ", "Description": "R utilities for gff files, either general feature format\n(GFF3) or gene transfer format (GTF) formatted files. This\npackage includes functions for producing summary stats, check\nfor consistency and sorting errors, conversion from GTF to GFF3\nformat, file sorting, visualization and plotting of feature\nhierarchy, and exporting user defined feature subsets to SAF\nformat. 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} ], "_exports": [ "%>%", "check_gff", "get_features", "gff_stats", "gff_stats_by_chr", "gtf_to_gff3", "plot_features", "saf_from_gff", "sort_gff" ], "_help": [ { "page": "check_gff", "title": "Test consistency and order of a GFF file", "topics": [ "check_gff" ] }, { "page": "get_features", "title": "Analyses the feature type hierarchy of a GFF file", "topics": [ "get_features" ] }, { "page": "gff_stats", "title": "Summarizes the number of features of each type in a GFF file", "topics": [ "gff_stats" ] }, { "page": "gff_stats_by_chr", "title": "Summarizes the number of elements of each type in each chromosome of a GFF file", "topics": [ "gff_stats_by_chr" ] }, { "page": "gtf_to_gff3", "title": "Converts a GTF file into a GFF3 file", "topics": [ "gtf_to_gff3" ] }, { "page": "plot_features", "title": "Plots or exports an image of the feature tree from a GFF file", "topics": [ "plot_features" ] }, { "page": "saf_from_gff", "title": "Creates a SAF file from a GTF/GFF3 features for the given pairs of blocks and features", "topics": [ "saf_from_gff" ] }, { "page": "sort_gff", "title": "Sorts a GTF/GFF3 file", "topics": [ "sort_gff" ] } ], "_rundeps": [ "cli", "data.tree", "dplyr", "generics", "glue", "jsonlite", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "rlang", "stringi", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "Using_Rgff.Rmd", "filename": "Using_Rgff.html", "title": "Using Rgff", "author": "Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Rafael Torres-Perez", "engine": "knitr::rmarkdown", "headings": [ "0. 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