{"id":24745822,"url":"https://github.com/bibymaths/codonanalyzer","last_synced_at":"2025-10-18T07:31:47.442Z","repository":{"id":273115919,"uuid":"918749912","full_name":"bibymaths/codonanalyzer","owner":"bibymaths","description":"A collection of Perl scripts for analyzing DNA and protein sequences, featuring tools for rare codon detection, GC content profiling, and hydropathy plotting, optimized for Escherichia coli datasets.","archived":false,"fork":false,"pushed_at":"2025-05-11T23:17:04.000Z","size":16837,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-11T23:18:26.379Z","etag":null,"topics":["codon-usage","dna-sequences","perl","protein"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bibymaths.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"publiccode":null,"codemeta":null}},"created_at":"2025-01-18T18:54:52.000Z","updated_at":"2025-05-11T23:16:55.000Z","dependencies_parsed_at":"2025-01-18T19:34:55.778Z","dependency_job_id":"5fd8fd95-0bd5-4326-89fc-c7fca374b2d8","html_url":"https://github.com/bibymaths/codonanalyzer","commit_stats":null,"previous_names":["bibymaths/codonanalyzer"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/bibymaths/codonanalyzer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fcodonanalyzer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fcodonanalyzer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fcodonanalyzer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fcodonanalyzer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bibymaths","download_url":"https://codeload.github.com/bibymaths/codonanalyzer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fcodonanalyzer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263141104,"owners_count":23420003,"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":["codon-usage","dna-sequences","perl","protein"],"created_at":"2025-01-28T03:29:53.717Z","updated_at":"2025-10-18T07:31:42.409Z","avatar_url":"https://github.com/bibymaths.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CodonAnalyzer\n \n[![Snakemake](https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15384943.svg)](https://doi.org/10.5281/zenodo.15384943)\n \nOriginally developed using Perl in 2015, this pipeline has been modernized in 2025 with reproducibility and modularity in mind.\n\n---\n\n## Features\n\n- Codon usage statistics and GC content\n- Longest ORF extraction\n- Protein sequence translation\n- Hydropathy calculation (Kyte–Doolittle)\n- Plotting via Python + Matplotlib\n- Configurable via `config.yaml`\n- Reproducible workflow using Snakemake\n\n---\n\n## Quickstart\n\n```bash\ngit clone https://github.com/yourusername/codonanalyzer.git\ncd codonanalyzer\n``` \n### Setup Environment \n\n```bash \nconda install -c conda-forge -c bioconda snakemake matplotlib numpy=1.26.0\n```  \n\nor using environment.yml: \n\n```bash \nconda env create -f environment.yml \n``` \n\nThen, run:\n\n```bash\nsnakemake --cores 1\n```\n\n---\n\n## Documentation\n\nSee the full documentation [here](https://bibymaths.github.io/codonanalyzer).\n\n---\n\n## Author\n\n**Abhinav Mishra**  \nEmail: [mishraabhinav@gmail.com](mailto:mishraabhinav@gmail.com)\n\nFor full historical context, see [About](docs/about.md).\n\n---\n\n## License\n\nBSD 3-Clause. See [LICENSE](LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fcodonanalyzer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbibymaths%2Fcodonanalyzer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fcodonanalyzer/lists"}