About Anaconda Help Download Anaconda

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  16 days and 19 hours ago 67 main
conda 392.2 kB | noarch/r-soniclength-1.4.7-r44hc72bb7e_4.conda  16 days and 19 hours ago 63 main
conda 390.8 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_3.conda  1 year and 3 months ago 1097 main
conda 392.4 kB | noarch/r-soniclength-1.4.7-r44hc72bb7e_3.conda  1 year and 3 months ago 1042 main
conda 391.1 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_2.conda  2 years and 3 months ago 1505 main
conda 391.3 kB | noarch/r-soniclength-1.4.7-r43hc72bb7e_2.conda  2 years and 3 months ago 1520 main
conda 406.3 kB | noarch/r-soniclength-1.4.7-r42hc72bb7e_1.tar.bz2  2 years and 11 months ago 1787 main
conda 406.2 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_1.tar.bz2  2 years and 11 months ago 1757 main
conda 404.8 kB | noarch/r-soniclength-1.4.7-r40hc72bb7e_0.tar.bz2  4 years and 20 days ago 2464 main
conda 405.0 kB | noarch/r-soniclength-1.4.7-r41hc72bb7e_0.tar.bz2  4 years and 20 days ago 2520 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r40hc72bb7e_2.tar.bz2  4 years and 4 months ago 2453 main
conda 302.6 kB | noarch/r-soniclength-1.4.6-r41hc72bb7e_2.tar.bz2  4 years and 4 months ago 2419 main
conda 302.8 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_2.tar.bz2  5 years and 4 months ago 3222 main
conda 302.1 kB | noarch/r-soniclength-1.4.6-r40h6115d3f_2.tar.bz2  5 years and 4 months ago 3228 main
conda 301.5 kB | noarch/r-soniclength-1.4.6-r35h6115d3f_1.tar.bz2  6 years and 2 months ago 4120 main cf202003
conda 302.6 kB | noarch/r-soniclength-1.4.6-r36h6115d3f_1.tar.bz2  6 years and 2 months ago 4127 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.6-r351h6115d3f_0.tar.bz2  6 years and 3 months ago 4126 main cf202003
conda 301.5 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_1000.tar.bz2  6 years and 9 months ago 4647 main cf202003 gcc7 cf201901
conda 301.7 kB | noarch/r-soniclength-1.4.4-r351h6115d3f_0.tar.bz2  6 years and 9 months ago 4737 main cf202003 gcc7 cf201901

© 2025 Anaconda, Inc. All Rights Reserved. (v4.2.2) Legal | Privacy Policy