{"id":28321671,"url":"https://github.com/felixernst/modstrings","last_synced_at":"2025-06-16T14:09:15.963Z","repository":{"id":73649320,"uuid":"163859137","full_name":"FelixErnst/Modstrings","owner":"FelixErnst","description":":package: Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides.","archived":false,"fork":false,"pushed_at":"2024-03-26T21:21:09.000Z","size":697,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"devel","last_synced_at":"2025-06-01T20:53:14.341Z","etag":null,"topics":["bioconductor","biostrings","dna","dna-modifications","modified-nucleotides","nucleotides","rna","rna-modification-alphabet","rna-modifications","sequences"],"latest_commit_sha":null,"homepage":"https://felixernst.github.io/Modstrings/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/FelixErnst.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2019-01-02T15:38:41.000Z","updated_at":"2022-08-13T19:00:24.000Z","dependencies_parsed_at":null,"dependency_job_id":"6cd044f4-b7cd-4f9e-a691-1cf98ff02406","html_url":"https://github.com/FelixErnst/Modstrings","commit_stats":{"total_commits":138,"total_committers":4,"mean_commits":34.5,"dds":0.4782608695652174,"last_synced_commit":"84fb6b7541e724c6a8cfdd71a3e75699f6242eda"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/FelixErnst/Modstrings","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixErnst%2FModstrings","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixErnst%2FModstrings/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixErnst%2FModstrings/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixErnst%2FModstrings/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FelixErnst","download_url":"https://codeload.github.com/FelixErnst/Modstrings/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixErnst%2FModstrings/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260174102,"owners_count":22969871,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","biostrings","dna","dna-modifications","modified-nucleotides","nucleotides","rna","rna-modification-alphabet","rna-modifications","sequences"],"created_at":"2025-05-25T12:15:16.043Z","updated_at":"2025-06-16T14:09:15.953Z","avatar_url":"https://github.com/FelixErnst.png","language":"R","readme":"# Modstrings: working with modified nucleotide sequences \u003cimg src=\"https://raw.githubusercontent.com/Bioconductor/BiocStickers/devel/Modstrings/Modstrings.png\" height=\"200\" align=\"right\"\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check-bioc-devel](https://github.com/FelixErnst/Modstrings/workflows/R-CMD-check-bioc-devel/badge.svg)](https://github.com/FelixErnst/Modstrings/actions/)\n[![BioC Build](https://bioconductor.org/shields/build/devel/bioc/Modstrings.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/)\n[![codecov](https://codecov.io/gh/FelixErnst/Modstrings/branch/devel/graph/badge.svg)](https://codecov.io/gh/FelixErnst/Modstrings)\n[![BioC Years](https://bioconductor.org/shields/years-in-bioc/Modstrings.svg)](https://doi.org/doi:10.18129/B9.bioc.Modstrings)\n\u003c!-- badges: end --\u003e\n\nRNA are usually in some form post-transcriptionally modified. Most prominent\nexamples are of course rRNA and tRNA, but in recent years mRNA was also\ndiscovered to be post-transcriptionally modified.\n\nIn many resources, like the tRNAdb ([Juehling et al. 2009](#Literature)) or the\nmodomics database ([Boccaletto et al. 2018](#Literature)), a dictionary for\nmodified nucleotides was published. However, in the Bioconductor universe these\ninformation were not directly accessible or representable, since they rely \nextensively on special characters in the RNA modification alphabet.\n\nTherefore, the`Modstrings` package implements the `ModRNAString` class by\nextending the `BString` class from the `Biostrings` ([Pages et\nal.](#Literature)) package. It can store RNA sequences containing special\ncharacters of the RNA modification alphabet and thus can store location and \nidentity of modifications. Functions for conversion to a tabular format are \nimplemented as well. A `ModDNAString` class is implemented analogously, which\nis based on the DNA modification alphabet from the Hoffman lab ([Sood et\nal.](#Literature)).\n\nThe implemented classes inherit most of the functions from the parental \n`BString` class and it derivatives, which allows them to behave like the \nnormal `XString` classes within the bioconductor universe.\n\n# Installation\n\nThe current version of the `Modstrings` package is available from \nBioconductor.\n \n```{r}\n# Installation\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"Modstrings\")\n# Load and attach the package\nlibrary(\"Modstrings\")\n```\n\n# Literature\n\n- Jühling, Frank; Mörl, Mario; Hartmann, Roland K.; Sprinzl, Mathias; Stadler,\nPeter F.; Pütz, Joern (2009): \"TRNAdb 2009: Compilation of tRNA Sequences and\ntRNA Genes.\" Nucleic Acids Research 37 (suppl_1): D159–D162.\ndoi:[10.1093/nar/gkn772](https://doi.org/10.1093/nar/gkn772). \n- Boccaletto, Pietro; Machnicka, Magdalena A.; Purta, Elzbieta; Piatkowski,\nPawel; Baginski, Blazej; Wirecki, Tomasz K. et al. (2018): \"MODOMICS: a database\nof RNA modification pathways. 2017 update.\" Nucleic Acids Res. 46 (D1),\nD303-D307. doi:[10.1093/nar/gkx1030](https://doi.org/10.1093/nar/gkx1030).\n- Pagès, H.; Aboyoun, P.; Gentleman, R.; DebRoy, S. (2018). \"Biostrings: \nEfficient manipulation of biological strings.\" R package version 2.50.1.\n- Sood, Ankur Jai, Coby Viner, and Michael M. Hoffman. 2019. “DNAmod: The Dna \nModification Database.” Journal of Cheminformatics 11 (1):30. \ndoi:[10.1186/s13321-019-0349-4](https://doi.org/10.1186/s13321-019-0349-4).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffelixernst%2Fmodstrings","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffelixernst%2Fmodstrings","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffelixernst%2Fmodstrings/lists"}