{ "_id": "6a1ee392b401979e73410f33", "Package": "sonicLength", "Type": "Package", "Title": "Estimating Abundance of Clones from DNA Fragmentation Data", "Version": "1.4.7", "Date": "2021-09-19", "Author": "Charles Berry ", "Maintainer": "Charles Berry ", "Description": "Estimate the abundance of cell clones from the\ndistribution of lengths of DNA fragments (as created by\nsonication, whence `sonicLength'). The algorithm in\n\"Estimating abundances of retroviral insertion sites from DNA\nfragment length data\" by Berry CC, Gillet NA, Melamed A,\nGormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar\n15;28(6):755-62 is implemented. The experimental setting and\nestimation details are described in detail there. Briefly,\nintegration of new DNA in a host genome (due to retroviral\ninfection or gene therapy) can be tracked using DNA sequencing,\npotentially allowing characterization of the abundance of\nindividual cell clones bearing distinct integration sites. The\nlocations of integration sites can be determined by fragmenting\nthe host DNA (via sonication or fragmentase), breaking the\nnewly integrated DNA at a known sequence, amplifying the\nfragments containing both host and integrated DNA, sequencing\nthose amplicons, then mapping the host sequences to positions\non the reference genome. The relative number of fragments\ncontaining a given position in the host genome estimates the\nrelative abundance of cells hosting the corresponding\nintegration site, but that number is not available and the\ncount of amplicons per fragment varies widely. However, the\nexpected number of distinct fragment lengths is a function of\nthe abundance of cells hosting an integration site at a given\nposition and a certain nuisance parameter. The algorithm\nimplicitly estimates that function to estimate the relative\nabundance.", "License": "GPL (>= 2)", "LazyLoad": "yes", "Repository/R-Forge/Project": "soniclength", "Repository/R-Forge/Revision": "12", "Repository/R-Forge/DateTimeStamp": "2021-09-19 22:55:50", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 06:26:18 UTC", "User": "root" }, "Repository": "https://chasberry.r-universe.dev", "Date/Publication": "2021-09-20 03:10:02 UTC", "RemoteUrl": "https://github.com/cran/sonicLength", "RemoteRef": "HEAD", "RemoteSha": "bf5c40be8ccf40bf01eccbd1de30e6a991477e5d", "MD5sum": "e2df947021a752e0fc7e37c5be44e72e", "_user": "chasberry", "_type": "src", "_file": "sonicLength_1.4.7.tar.gz", "_fileid": "6f0b9d1a41a6d30dbc1ac057bd901263aa1d26d76f725ea048c1bfe051aae818", "_filesize": 408567, "_sha256": "6f0b9d1a41a6d30dbc1ac057bd901263aa1d26d76f725ea048c1bfe051aae818", "_created": "2026-05-20T06:26:18.000Z", "_published": "2026-06-02T14:07:14.482Z", "_distro": "noble", 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"time": 79, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7102774661" } ], "_buildurl": "https://github.com/r-universe/chasberry/actions/runs/26145323051", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/sonicLength", "_commit": { "id": "bf5c40be8ccf40bf01eccbd1de30e6a991477e5d", "author": "Charles Berry ", "committer": "cran-robot ", "message": "version 1.4.7\n", "time": 1632107402 }, "_maintainer": { "name": "Charles Berry", "email": "ccberry@ucsd.edu", "login": "chasberry", "description": "", "uuid": 1952008 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.14.0", "role": "Depends" }, { "package": "splines", "role": "Depends" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "chasberry", "count": 3, "uuid": 1952008 } ], "_userbio": { "uuid": 1952008, "type": "user", "name": "chasberry" }, "_downloads": { "count": 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