{"id":19624133,"url":"https://github.com/bioconductor/copy-number-analysis","last_synced_at":"2025-04-28T05:31:18.618Z","repository":{"id":13634055,"uuid":"16327392","full_name":"Bioconductor/copy-number-analysis","owner":"Bioconductor","description":"Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis","archived":false,"fork":false,"pushed_at":"2023-03-15T20:24:45.000Z","size":2542,"stargazers_count":21,"open_issues_count":2,"forks_count":12,"subscribers_count":22,"default_branch":"devel","last_synced_at":"2024-05-09T07:48:41.235Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.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":"2014-01-28T21:58:05.000Z","updated_at":"2023-08-24T18:56:18.000Z","dependencies_parsed_at":"2022-09-12T08:20:46.860Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/copy-number-analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fcopy-number-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fcopy-number-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fcopy-number-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fcopy-number-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/copy-number-analysis/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096863,"owners_count":17255173,"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":"2024-11-11T11:37:05.162Z","updated_at":"2024-11-11T11:37:06.252Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"Copy Number Analysis \n=====================\n\nExplore, compare, and evaluate Bioconductor packages related to genomic copy number analysis\n\nGenomic amplifications and deletions are found in most (all?) tumor genomes.  A common practice today is to do low coverage DNA sequencing (0.5x, for instance) of a tumor genome, and a matched normal genome (from the same subject).  Judicious comparison of the the two sequence genomes illuminates structural changes in the tumor.\n\nCopy number changes in tumors vary from broad (an entire chromosome arm) to focal (i.e., a 10kb amplification, loss of heterozygosity or gain).   Detection methods should be sensitive enough to detect these very different phenomena in noisy low-coverage data.\n\nOur purpose here is to provide\n\n* A tumor/normal single chromosome pair of bam files (with accompanying index files)\n* A reference analysis, using the popular SeqSeg matlab program from the Broad Institute\n* A tutorial on the exploratory data analysis of these files using \"native\" Bioconductor capabilities\n* Demonstrate (and evaluate) the capabilities of many of the Bioconductor copy number analysis packages\n\nList of Tools used\n===================\nBioconductor Packages\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/CountOverlaps-method-from-IRanges-Package\"\u003ecountOverlaps\u003c/a\u003e\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/cn.mops\"\u003ecn.mops\u003c/a\u003e\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/CNAnorm\"\u003eCNAnorm\u003c/a\u003e\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/seqCNA\"\u003eseqCNA\u003c/a\u003e\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/HMMcopy\"\u003eHMMcopy\u003c/a\u003e  \n* \u003ca href =\"https://github.com/Bioconductor/copy-number-analysis/wiki/TitanCNA\"\u003eTitanCNA\u003c/a\u003e\n\u003cbr\u003e\n\nNon Biocondcutor packages\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/CNV-seq\"\u003eCNV-seq\u003c/a\u003e\n* \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/SegSeq\"\u003eSeg-seq\u003c/a\u003e\n\n\nLiterature Resources\n=========================\n* Alkan, C., et al. (2011). \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/21358748\"\u003e\"Genome structural variation discovery and genotyping.\"\u003c/a\u003e Nat Rev Genet 12(5): 363-376. \n* Duan J, Zhang J-G, Deng H-W, Wang Y-P (2013) \u003ca href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059128\"\u003eComparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies.\u003c/a\u003e PLoS ONE 8(3): e59128. doi:10.1371/journal.pone.0059128\n\nSample Data\n===========\n* http://s3.amazonaws.com/copy-number-analysis/tumorA.chr4.bam\n* http://s3.amazonaws.com/copy-number-analysis/tumorA.chr4.bam.bai\n* http://s3.amazonaws.com/copy-number-analysis/normalA.chr4.bam\n* http://s3.amazonaws.com/copy-number-analysis/normalA.chr4.bam.bai\n\nUse, e.g.,\n\u003cpre\u003e\u003ccode\u003e \ndownload.file(url=\"http://s3.amazonaws.com/copy-number-analysis/tumorA.chr4.bam.bai\",\n              destfile=\"tumorA.chr4.bam.bai\")\n\u003c/code\u003e\u003c/pre\u003e\n\n\nExploratory Data Analysis\n==========================\nWe have done some primary \u003ca href=\"https://github.com/Bioconductor/copy-number-analysis/wiki/Exploratory-Data-Analysis\"\u003eExploratory Data Analysis\u003c/a\u003e on the Normal and Tumor Sample Datasets.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fcopy-number-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fcopy-number-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fcopy-number-analysis/lists"}