{"id":20425032,"url":"https://github.com/databio/fused","last_synced_at":"2026-04-18T12:35:19.474Z","repository":{"id":86287776,"uuid":"446871236","full_name":"databio/FUSED","owner":"databio","description":"FUSion Error prone repair Detection","archived":false,"fork":false,"pushed_at":"2022-05-05T15:40:06.000Z","size":116,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-11T10:16:14.386Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/databio.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":"2022-01-11T15:14:56.000Z","updated_at":"2022-04-15T11:01:04.000Z","dependencies_parsed_at":"2023-03-13T09:28:30.494Z","dependency_job_id":null,"html_url":"https://github.com/databio/FUSED","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/databio/FUSED","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FFUSED","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FFUSED/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FFUSED/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FFUSED/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/databio","download_url":"https://codeload.github.com/databio/FUSED/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/databio%2FFUSED/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31969762,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-18T00:39:45.007Z","status":"online","status_checked_at":"2026-04-18T02:00:07.018Z","response_time":103,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-15T07:12:03.864Z","updated_at":"2026-04-18T12:35:19.454Z","avatar_url":"https://github.com/databio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"FUSED_logo.svg\" alt=\"FUSED logo\" height=\"200\" align=\"left\"/\u003e  \n\n\u003cbr\u003e\u003c/br\u003e\n\u003cbr\u003e\u003c/br\u003e\n\u003cbr\u003e\u003c/br\u003e\n\n**FUS**ion **E**rror-prone repair **D**etection\n\n## Description\n\nFUSED is a collection of functions to determine the presence of hallmarks of common DNA repair mechanisms including NHEJ, MMEJ, SSA, BIR, and MMBIR. \n\n\u003cimg src=\"Microhomology_Error_Prone_Repair_Spectrum.svg\" alt=\"error prone repair cartoon\" height=\"450\" align=\"center\"/\u003e \n\n### NHEJ\n\nFor non-homologous end-joining, FUSED looks for homology between 1-4nt (nt==nucleotide) in length between the left fusion gene and the right fusion gene in a window up to 4nt away from the breakpoint. It requires the homology to be anchored *at* the breakpoint.\n\n### SSA\n\nFor single-strand annealing, FUSED looks for homology between 30 and 70nt in length in a window around the breakpoint up to 70nt away on both sides of the breakpoint.\n\n### MMEJ\n\nFor microhomology-mediated end joining, FUSED looks for homology between 1-20nt in length between the left fusion gene and the right fusion gene in a window up to 50nt away from the breakpoint. \n\n### BIR\n\nFor break-induced replication, FUSED looks for homology between 70-100nt in length in a window 100nt upstream and downstream of the breakpoint.\n\n### MMBIR\n\nFor microhomology-mediated break-induced replication, FUSED looks for homology between 1-20nt in length in a window 20nt upstream and downstream of the breakpoint. It requires the homology to be anchored *at* the breakpoint, expects a gapped alignment of at least a single nt but with at least 80% overall homology.\n\n## Input\n\nFUSED expects a fusion prediction file from either: STAR, ARRIBA, or ORIEN derived pipelines. It utilizes a BSgenome object (or string) to pull matching sequence information from the coordinates of the predicted fusion. It can evaluate 5 different possible error repair mechanisms: NHEJ, MMEJ, SSA, BIR, or MMBIR.\n\n## Usage\n\n```R\ndevtools::install_github(\"databio/FUSED\")\nlibrary(FUSED)\ninputDT \u003c- fread(\"ORIEN-FusionBreakpoints.txt\")\ncalcHomology(inputDT, mechanism=\"NHEJ\", bsg=\"BSgenome.Hsapiens.UCSC.hg38\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Ffused","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabio%2Ffused","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabio%2Ffused/lists"}