{"id":20083731,"url":"https://github.com/y9c/m6a-camseq","last_synced_at":"2025-05-06T01:31:34.184Z","repository":{"id":245010823,"uuid":"809487005","full_name":"y9c/m6A-CAMseq","owner":"y9c","description":"🧪 m6A-CAM-seq","archived":false,"fork":false,"pushed_at":"2025-02-28T18:29:18.000Z","size":6605,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-09T06:35:03.833Z","etag":null,"topics":["bioinformatics","epigenetics","rna"],"latest_commit_sha":null,"homepage":"https://camseq.chuan.science","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/y9c.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":"2024-06-02T20:29:24.000Z","updated_at":"2025-03-27T19:21:57.000Z","dependencies_parsed_at":"2024-06-19T02:13:16.137Z","dependency_job_id":"c2711306-b889-4a05-bdaa-a4a543e0949c","html_url":"https://github.com/y9c/m6A-CAMseq","commit_stats":null,"previous_names":["y9c/m6a-camseq"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-CAMseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-CAMseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-CAMseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/y9c%2Fm6A-CAMseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/y9c","download_url":"https://codeload.github.com/y9c/m6A-CAMseq/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252604298,"owners_count":21775079,"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":["bioinformatics","epigenetics","rna"],"created_at":"2024-11-13T15:48:37.249Z","updated_at":"2025-05-06T01:31:34.176Z","avatar_url":"https://github.com/y9c.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# m\u003csup\u003e6\u003c/sup\u003eA-CAMseq\n\n![diagram](./docs/diagram.svg)\n\n## Qucik start\n\n- Prepare configuration file\n\n_minimum configuration example:_\n\n```yaml\nreference:\n  genes:\n    - ./ref/spike-in.fa\n    - ./ref/Arabidopsis_thaliana.rRNA.fa\n  genome:\n    - /data/reference/genome/Arabidopsis_thaliana/TAIR10.fa\n\n# TODO: automatically generate index (?)\ngenome_index: /data/reference/genome/Arabidopsis_thaliana/hisat2_tx_3n/TAIR10.release57\n\nsamples:\n  test1:\n    - R1: ../test/test_R1.fq.gz\n      R2: ../test/test_R2.fq.gz\n```\n\n_advanced configuration:_\n\n```yaml\n# set library preparation method\n# can be \"STRANDED\", \"ECLIP10\", etc, refer to the cutseq documentation for more information\nlibtype: STRANDED\n\n# by default, the pipeline will use the strandness information from the library\n# if the strandness is not available, set the strandness to `false`\nstrandness: true\n\n# by default, the pipeline will force remove the PCR duplicates based on the UMI\n# if UMI is not available, you can toggle the markdup to `false` to skip the PCR duplicate removal\nmarkdup: true\n```\n\n- Install apptainer and run\n\n```bash\napptainer run -B /data docker://y9ch/camseq -c data.yaml -j 48\n```\n\n## Customization\n\nSystem Requirements\n\nThis package has been tested on Linux operating systems. It requires the following software dependencies:\n\n- [Python](https://www.python.org/downloads/) 3.7 or higher\n- [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) 8.0.0 or higher\n- [hisat2-3n](https://github.com/DaehwanKimLab/hisat2/tree/hisat-3n)\n- cutseq\n\n## Documentation\n\nThe documentation is available at [https://y9c.github.io/m6A-CAMseq/](https://y9c.github.io/m6A-CAMseq/)\n\n\u0026nbsp;\n\n\u003cp align=\"center\"\u003e\n\u003cimg\n  src=\"https://raw.githubusercontent.com/y9c/y9c/master/resource/footer_line.svg?sanitize=true\"\n/\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\nCopyright \u0026copy; 2023-present\n\u003ca href=\"https://github.com/y9c\" target=\"_blank\"\u003eChang Y\u003c/a\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fm6a-camseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fy9c%2Fm6a-camseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fm6a-camseq/lists"}