{"id":25953869,"url":"https://github.com/biomystery/ataccnv","last_synced_at":"2026-05-09T08:10:41.423Z","repository":{"id":75029123,"uuid":"136091334","full_name":"biomystery/atacCNV","owner":"biomystery","description":"A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data","archived":false,"fork":false,"pushed_at":"2018-06-04T23:29:42.000Z","size":16,"stargazers_count":3,"open_issues_count":4,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-04T15:46:25.109Z","etag":null,"topics":["atac-seq","bioinformatics","cnv"],"latest_commit_sha":null,"homepage":"","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/biomystery.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,"publiccode":null,"codemeta":null}},"created_at":"2018-06-04T22:51:40.000Z","updated_at":"2022-11-13T20:44:32.000Z","dependencies_parsed_at":"2023-06-28T17:31:16.462Z","dependency_job_id":null,"html_url":"https://github.com/biomystery/atacCNV","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/biomystery/atacCNV","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomystery%2FatacCNV","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomystery%2FatacCNV/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomystery%2FatacCNV/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomystery%2FatacCNV/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biomystery","download_url":"https://codeload.github.com/biomystery/atacCNV/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomystery%2FatacCNV/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32811686,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-08T08:22:46.396Z","status":"online","status_checked_at":"2026-05-09T02:00:06.633Z","response_time":123,"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":["atac-seq","bioinformatics","cnv"],"created_at":"2025-03-04T15:36:58.976Z","updated_at":"2026-05-09T08:10:41.415Z","avatar_url":"https://github.com/biomystery.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# atacCNV\n\nCall Copy Number Variation from ATAC-seq data. \n\n## Useage\n\n```Shell\nexport PATH=$PATH:$(pwd)\n```\n\n## List of files \n\n* [bedToBdgBW.sh](./src/bedToBdgBw.sh): use `macs pileup` to generate pileup track (`bw`,`bdg`) from input reads (`bed`)  with reads extend half of window size in both direction. \n* [tagToFrag.sh](./src/tagToFrag.sh): covert `tagAlign` to fragments in `bed`, `sort.bdg` and `bw`  format. \n* [readsMasker.sh](./src/readsMasker.sh): filter reads (in `bed` format) by given mask regions. \n* [smoothBw.sh](./src/smoothBw.sh): smooth bigwig by sliding window (size - w and step - s)\n* [callCNV.R](./src/callCNV.R): call CNV from treat adjusted by mapb \n\n\n## Typical Steps:\n\n1. Get output from pipleine: `tagAlign`, `peaks` (openning regions).\n2. (optional) Run [tagToFrag.sh](./src/tagToFrag.sh): get fragments `bed`, `bdg` and `bw`\n3. Run [readsMasker.sh](./src/readsMasker.sh) to filter out reads or frags in peak regions and get background frags. \n4. Run [smoothBw.sh](./src/smoothBw.sh) to get average coverage in each window for both control or treatment. It will reorder the bed file, so that the it cannot preserve the pair info if input is in  `tagAlign` format. Please covert to fragment bed first. \n5. Run [callCNV.R](callCNV.R) to get CNV regions, segment plots \n\n## Call Wrapper: \n* Input: reads (`tagAlign`), peak regions (`bed` or `narrowPeaks`), mapb track (`bw`), sliding window (`stepsize`,`windowsize`)\n* Output: CNV regions (`bed`), log2CovRaito plots with segments (`pngs` and `tab`), background reads track (`bw`) \n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomystery%2Fataccnv","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiomystery%2Fataccnv","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomystery%2Fataccnv/lists"}