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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-staging / r-soniclength
Type Size Name Uploaded Downloads Labels
conda 390.8 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_3.conda  1 year and 1 month ago 1023 main
conda 392.4 kB | noarch/r-soniclength-1.4.7-r44hc72bb7e_3.conda  1 year and 1 month ago 972 main
conda 391.1 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_2.conda  2 years and 2 months ago 1430 main
conda 391.3 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_2.conda  2 years and 2 months ago 1443 main
conda 406.3 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_1.tar.bz2  2 years and 10 months ago 1716 main
conda 406.2 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_1.tar.bz2  2 years and 10 months ago 1687 main
conda 404.8 kB | noarch/r-soniclength-1.4.7-r40hc72bb7e_0.tar.bz2  3 years and 11 months ago 2395 main
conda 405.0 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_0.tar.bz2  3 years and 11 months ago 2458 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r40hc72bb7e_2.tar.bz2  4 years and 3 months ago 2377 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r41hc72bb7e_2.tar.bz2  4 years and 3 months ago 2351 main
conda 302.8 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_2.tar.bz2  5 years and 3 months ago 3153 main
conda 302.1 kB | noarch/r-soniclength-1.4.6-r40h6115d3f_2.tar.bz2  5 years and 3 months ago 3158 main
conda 301.5 kB | noarch/r-soniclength-1.4.6-r35h6115d3f_1.tar.bz2  6 years and 1 month ago 4051 main cf202003
conda 302.6 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_1.tar.bz2  6 years and 1 month ago 4056 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.6-r351h6115d3f_0.tar.bz2  6 years and 1 month ago 4054 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_1000.tar.bz2  6 years and 8 months ago 4570 main cf202003 gcc7 cf201901
conda 301.7 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_0.tar.bz2  6 years and 8 months ago 4663 main cf202003 gcc7 cf201901

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