{"id":13710278,"url":"https://github.com/bartongroup/differr_nanopore_DRS","last_synced_at":"2025-05-06T18:34:55.441Z","repository":{"id":50748552,"uuid":"169076748","full_name":"bartongroup/differr_nanopore_DRS","owner":"bartongroup","description":"Scripts for identifying sites with differential error rates in mapped nanopore DRS data","archived":false,"fork":false,"pushed_at":"2020-11-27T09:29:12.000Z","size":16,"stargazers_count":11,"open_issues_count":1,"forks_count":3,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-11-22T01:15:20.771Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","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/bartongroup.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}},"created_at":"2019-02-04T12:42:25.000Z","updated_at":"2024-10-28T03:56:39.000Z","dependencies_parsed_at":"2022-09-02T22:11:37.736Z","dependency_job_id":null,"html_url":"https://github.com/bartongroup/differr_nanopore_DRS","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bartongroup%2Fdifferr_nanopore_DRS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bartongroup%2Fdifferr_nanopore_DRS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bartongroup%2Fdifferr_nanopore_DRS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bartongroup%2Fdifferr_nanopore_DRS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bartongroup","download_url":"https://codeload.github.com/bartongroup/differr_nanopore_DRS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252745034,"owners_count":21797723,"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":[],"created_at":"2024-08-02T23:00:53.940Z","updated_at":"2025-05-06T18:34:55.094Z","avatar_url":"https://github.com/bartongroup.png","language":"Python","funding_links":[],"categories":["Software packages"],"sub_categories":["RNA modification analysis"],"readme":"## A tool for detecting modifications from Nanopore DRS errors using a low modification control\n\n### How to use:\n* Basecall \u0026 map direct RNA data (all datasets **MUST** be sequenced at approximately the same time with the exactly the same flowcell/kit/MinKNOW software, and basecalled and mapped in the same way with the same model, otherwise you **WILL** get loads of false positives. Nanopore update their pores/kits/models/software all the time, so be wary...).\n* Run `differr` on mapped bam files.\n* Output from `differr` is a bed file with the positions with significantly altered error, and a optional hdf5 file with all of the per reference base basecalls, which might be useful for further analyses.\n* Columns of bed file are:\n    * chrom, start, end, name\n    * score: -log10 of the FDR, rounded to nearest whole number\n    * strand\n    * odds ratio: the change in the ratio of matches to mismatches in the wild type compared to the mutant with low modifications. An odds ratio \u003e 0 indicates more modifications in the WT.\n    * G statistic for the comparison of pooled WT and mutant samples.\n    * -log10 P value for the comparison of pooled WT and mutant samples.\n    * -log10 FDR for the comparison of pooled WT and mutant samples.\n    * G statistic for the homogeneity test of mutant replicates.\n    * -log10 P value for the homogeneity test of mutant replicates.\n    * G statistic for the homogeneity test of wild type replicates.\n    * -log10 P value for the homogeneity test of wild type replicates.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbartongroup%2Fdifferr_nanopore_DRS","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbartongroup%2Fdifferr_nanopore_DRS","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbartongroup%2Fdifferr_nanopore_DRS/lists"}