{ "_id": "6a1f2b79b401979e73425566", "Package": "GencoDymo2", "Type": "Package", "Title": "Comprehensive Analysis of 'GENCODE' Annotations and Splice Site\nMotifs", "Version": "1.0.4", "Authors@R": "c(\nperson(\"Monah\", \"Abou Alezz\", email = \"aboualezz.monah@hsr.it\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-2006-4250\")),\nperson(\"Lorenzo\", \"Salviati\", email = \"lorenzo.salviati01@universitadipavia.it\", role = \"ctb\"),\nperson(\"Roberta\", \"Alfieri\", email = \"roberta.alfieri@igm.cnr.it\", role = \"ctb\"),\nperson(\"Silvia\", \"Bione\", email = \"bione@igm.cnr.it\", role = \"ctb\"))", "Maintainer": "Monah Abou Alezz ", "Description": "A comprehensive suite of helper functions designed to\nfacilitate the analysis of genomic annotations from the\n'GENCODE' database , supporting\nboth human and mouse genomes. This toolkit enables users to\nextract, filter, and analyze a wide range of annotation\nfeatures including genes, transcripts, exons, and introns\nacross different 'GENCODE' releases. It provides functionality\nfor cross-version comparisons, allowing researchers to\nsystematically track annotation updates, structural changes,\nand feature-level differences between releases. In addition,\nthe package can generate high-quality FASTA files containing\ndonor and acceptor splice site motifs, which are formatted for\ndirect input into the 'MaxEntScan' tool (Yeo and Burge, 2004\n), enabling accurate calculation\nof splice site strength scores.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/monahton/GencoDymo2,\nhttps://monahton.github.io/GencoDymo2/", "BugReports": "https://github.com/monahton/GencoDymo2/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://monahton.r-universe.dev", "Date/Publication": "2026-02-05 19:13:24 UTC", "RemoteUrl": "https://github.com/monahton/GencoDymo2", "RemoteRef": "main", "RemoteSha": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 10:16:16 UTC", "User": "root" }, "Author": "Monah Abou Alezz [aut, cre, cph] (ORCID:\n),\nLorenzo Salviati [ctb],\nRoberta Alfieri [ctb],\nSilvia Bione [ctb]", "MD5sum": "85971e015c9589622583ba4f991b5b41", "_user": "monahton", "_type": "src", "_file": "GencoDymo2_1.0.4.tar.gz", "_fileid": "6a154c9769c880b6a058539193955d09e5004dba0cc5987bf0764e24248cabd9", "_filesize": 327368, "_sha256": "6a154c9769c880b6a058539193955d09e5004dba0cc5987bf0764e24248cabd9", "_created": "2026-05-15T10:16:16.000Z", "_published": "2026-06-02T19:14:01.412Z", "_distro": "noble", "_jobs": [ { "job": 79151665724, "time": 390, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7014992011" }, { "job": 79151665951, "time": 400, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7014994761" }, { "job": 79151666186, "time": 305, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7015005361" }, { "job": 79151665672, "time": 216, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7014968940" }, { "job": 79151665753, "time": 332, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7014884969" }, { "job": 79151665153, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367446758" }, { "job": 79151665722, "time": 361, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7014983632" }, { "job": 79151666036, "time": 344, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7014979061" }, { "job": 79151666399, "time": 321, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7014973165" } ], "_buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/monahton/GencoDymo2", "_commit": { "id": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "author": "monahton ", "committer": "monahton ", "message": "add contributors\n", "time": 1770318804 }, "_maintainer": { "name": "Monah Abou Alezz", "email": "aboualezz.monah@hsr.it", "login": "monahaboualezz", "uuid": 89578888, "orcid": "0000-0002-2006-4250" }, "_registered": true, "_dependencies": [ { "package": "Biostrings", "version": ">= 2.72.1", "role": "Imports" }, { "package": "BSgenome", "version": ">= 1.66.3", "role": "Imports" }, { "package": "data.table", "version": ">= 1.17.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.4", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.56.2", "role": "Imports" }, { "package": "methods", "version": ">= 4.4.0", "role": "Imports" }, { "package": "plotrix", "version": ">= 3.8.4", "role": "Imports" }, { "package": "progress", "version": ">= 1.2.3", "role": "Imports" }, { "package": "RCurl", "version": ">= 1.98.1.17", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.64.0", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.38.1", "role": "Imports" }, { "package": "tools", "version": ">= 4.4.0", "role": "Imports" }, { "package": "utils", "version": ">= 4.4.0", "role": "Imports" }, { "package": "devtools", "version": ">= 2.4.5", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "version": ">= 1.4.5", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "monahton", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 4 }, { "week": "2025-21", "n": 1 }, { "week": "2025-28", "n": 4 }, { "week": "2025-29", "n": 3 }, { "week": "2025-34", "n": 4 }, { "week": "2026-03", "n": 5 }, { "week": "2026-06", "n": 2 } ], "_tags": [ { "name": "v1.0.2", "date": "2025-07-14" }, { "name": "v1.0.4", "date": "2026-01-12" } ], "_stars": 3, "_contributors": [ { "user": "monahton", "count": 19, "uuid": 38108817 }, { "user": "davisvaughan", "count": 1, "uuid": 19150088 }, { "user": "georgette-femerling", "count": 1, "uuid": 63737044 } ], "_userbio": { "uuid": 38108817, "type": "user", "name": "monahton", "description": "Dr. Monah Abou Alezz, PhD.\r\nComputational Biology | Postdoctoral researcher in gene therapy - San Raffaele Hospital | Bioinformatics trainer" }, "_downloads": { "count": 467, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GencoDymo2" }, "_devurl": "https://github.com/monahton/gencodymo2", "_pkgdown": "https://monahton.github.io/GencoDymo2/", "_searchresults": 5, "_metadata": { "review": { "status": "reviewed", "version": "1.0.1", "organization": "monahton", "url": "https://monahton.github.io/GencoDymo2/" } }, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GencoDymo2.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/monahton/gencodymo2", "_realowner": "monahton", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2025-05-15" }, { "version": "1.0.2", "date": "2025-07-14" }, { "version": "1.0.3", "date": "2025-08-21" }, { "version": "1.0.4", "date": "2026-01-12" } ], "_exports": [ "assign_splice_sites", "calculate_gc_content", "classify_exons", "compare_release", "df_to_fasta", "eliminate_redundant_elements", "extract_cds_sequences", "extract_element_by_strand", "extract_introns", "extract_single_exon", "extract_ss_motif", "find_cryptic_splice_sites", "get_gff3", "get_gtf", "get_latest_release", "load_file", "spliced_trans_length", "stat_summary" ], "_help": [ { "page": "assign_splice_sites", "title": "Assign intron donor and acceptor splice sites consensus", "topics": [ "assign_splice_sites" ] }, { "page": "calculate_gc_content", "title": "Calculate GC Content of Genomic Features", "topics": [ "calculate_gc_content" ] }, { "page": "classify_exons", "title": "Classify Exons by Their Relative Transcript Position", "topics": [ "classify_exons" ] }, { "page": "compare_release", "title": "Compare Annotation Counts Between Two GENCODE Releases", "topics": [ "compare_release" ] }, { "page": "df_to_fasta", "title": "Convert Data Frame to FASTA File", "topics": [ "df_to_fasta" ] }, { "page": "eliminate_redundant_elements", "title": "Eliminate Redundant Genomic Elements", "topics": [ "eliminate_redundant_elements" ] }, { "page": "extract_cds_sequences", "title": "Extract Coding Sequences (CDS) from GTF Annotations", "topics": [ "extract_cds_sequences" ] }, { "page": "extract_element_by_strand", "title": "Extract Genomic Elements by Strand", "topics": [ "extract_element_by_strand" ] }, { "page": "extract_introns", "title": "Extract Intron Coordinates from GENCODE Annotations", "topics": [ "extract_introns" ] }, { "page": "extract_single_exon", "title": "Identify Single-Exon Genes/Transcripts in GENCODE Data", "topics": [ "extract_single_exon" ] }, { "page": "extract_ss_motif", "title": "Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')", "topics": [ "extract_ss_motif" ] }, { "page": "find_cryptic_splice_sites", "title": "Identify Potential Cryptic Splice Sites.", "topics": [ "find_cryptic_splice_sites" ] }, { "page": "get_gff3", "title": "Download GFF3 File from the GENCODE Database", "topics": [ "get_gff3" ] }, { "page": "get_gtf", "title": "Download GTF File from the GENCODE Database", "topics": [ "get_gtf" ] }, { "page": "get_latest_release", "title": "Get the Latest Gencode Release Dynamically", "topics": [ "get_latest_release" ] }, { "page": "load_file", "title": "Load a GTF or GFF3 file from GENCODE as a data frame.", "topics": [ "load_file" ] }, { "page": "spliced_trans_length", "title": "Calculate Spliced Transcript Lengths", "topics": [ "spliced_trans_length" ] }, { "page": "stat_summary", "title": "Generate Summary Statistics for Genomic Elements", "topics": [ "stat_summary" ] }, { "page": "tiny_example_gtf_files", "title": "Tiny example GTF files", "topics": [ "tiny_example_gtf_files" ] } ], "_readme": "https://github.com/monahton/GencoDymo2/raw/main/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "BSgenome", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "dplyr", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "hms", "httr", "IRanges", "jsonlite", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "pillar", "pkgconfig", "plotrix", "prettyunits", "progress", "purrr", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "GencoDymo2_vignette.Rmd", "filename": "GencoDymo2_vignette.html", "title": "GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs", "author": "Monah Abou Alezz1, Lorenzo Salviati2, Roberta Alfieri3, Silvia Bione4", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Usage", "Latest Releases", "Download GTF/GFF3 Files", "Supported Annotation Types", "Load and Inspect", "Compare Releases", "Extract Introns Coordinates", "Extract Donor and Acceptor Splice Sites", "Identify Cryptic splice sites", "Extract splice sites motifs for MaxEntScan webtool", "Additional Utilities", "Single-Exon Features", "Exon Classification", "Spliced Transcript Length", "Summary Statistics", "GC Content Calculation", "Extract CDS Sequences", "Session Information", "References" ], "created": "2025-04-28 13:42:20", "modified": "2025-08-21 08:13:48", "commits": 10 } ], "_score": 5.3222192947339195, "_indexed": true, "_nocasepkg": "gencodymo2", "_universes": [ "monahton", "monahaboualezz" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-05-15T10:20:22.000Z", "distro": "noble", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "99425cdd89e986730215c6cc661e381e9505286a7661c141499c26cb333448d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.6.0", "os": "linux", "version": "1.0.4", "date": "2026-05-15T10:20:35.000Z", "distro": "noble", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "bb0efacc587d98ad0f52e03a3e0c3bcc54c3bbb5fa9f4937b1175042bed0f915", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-05-15T10:21:56.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "8b84fa4ad5c17f2a970d1cd0e5315fec3751161a7ec2309385040911a31b862f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.6.0", "os": "mac", "version": "1.0.4", "date": "2026-05-15T10:20:23.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "e84ae1fa4c23ae80ece8b445b2d444ccc916e3c59c133bb7b3d53715936de6ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.7.0", "os": "win", "version": "1.0.4", "date": "2026-05-15T10:19:51.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "0ad0eb9ef6a18f4d2e5ec1a796beeee76cb059487e599835abeae952ffc2cf07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.5.3", "os": "win", "version": "1.0.4", "date": "2026-05-15T10:19:38.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "8c51d8484bb682253a123c158bc0645a6c8acf67306fa5a7610f8bcc3a193fdd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.6.0", "os": "win", "version": "1.0.4", "date": "2026-05-15T10:19:27.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "d44a41aa86fae7095f5975323a5f1e616e01917c30ddcd7f1060e2a5d27fc0a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.4", "date": "2026-06-02T19:13:37.000Z", "commit": "98a2f4aba1c7fb686f9b4f223bf6f8cb3c9dfd27", "fileid": "b62540abedd4021ce6886f2b02d2ec3c1e86deb46956ab60f864d533b0493846", "status": "success", "buildurl": "https://github.com/r-universe/monahton/actions/runs/25912366118" } ] }