| Name : R-sonicLength
| |
| Version : 1.4.7
| Vendor : obs://build_opensuse_org/devel:languages:R
|
| Release : lp153.1.12
| Date : 2024-06-14 11:13:13
|
| Group : Development/Libraries/Other
| Source RPM : R-sonicLength-1.4.7-lp153.1.12.src.rpm
|
| Size : 0.41 MB
| |
| Packager : (none)
| |
| Summary : Estimating Abundance of Clones from DNA Fragmentation Data
|
Description :
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.
|
RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Leap_15.3/x86_64 |
