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Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.

copied from cf-post-staging / r-soniclength
Type Size Name Uploaded Downloads Labels
conda 392.1 kB | noarch/r-soniclength-1.4.7-r45hc72bb7e_4.conda  7 days and 20 hours ago 45 main
conda 392.2 kB | noarch/r-soniclength-1.4.7-r44hc72bb7e_4.conda  7 days and 20 hours ago 45 main
conda 390.8 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_3.conda  1 year and 2 months ago 1081 main
conda 392.4 kB | noarch/r-soniclength-1.4.7-r44hc72bb7e_3.conda  1 year and 2 months ago 1027 main
conda 391.1 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_2.conda  2 years and 3 months ago 1488 main
conda 391.3 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_2.conda  2 years and 3 months ago 1501 main
conda 406.3 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_1.tar.bz2  2 years and 11 months ago 1772 main
conda 406.2 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_1.tar.bz2  2 years and 11 months ago 1744 main
conda 404.8 kB | noarch/r-soniclength-1.4.7-r40hc72bb7e_0.tar.bz2  4 years and 11 days ago 2449 main
conda 405.0 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_0.tar.bz2  4 years and 11 days ago 2508 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r40hc72bb7e_2.tar.bz2  4 years and 4 months ago 2435 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r41hc72bb7e_2.tar.bz2  4 years and 4 months ago 2405 main
conda 302.8 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_2.tar.bz2  5 years and 4 months ago 3205 main
conda 302.1 kB | noarch/r-soniclength-1.4.6-r40h6115d3f_2.tar.bz2  5 years and 4 months ago 3213 main
conda 301.5 kB | noarch/r-soniclength-1.4.6-r35h6115d3f_1.tar.bz2  6 years and 2 months ago 4107 main cf202003
conda 302.6 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_1.tar.bz2  6 years and 2 months ago 4113 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.6-r351h6115d3f_0.tar.bz2  6 years and 2 months ago 4111 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_1000.tar.bz2  6 years and 9 months ago 4632 main cf202003 gcc7 cf201901
conda 301.7 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_0.tar.bz2  6 years and 9 months ago 4724 main cf202003 gcc7 cf201901

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