Changes between Version 38 and Version 39 of se.lu.onk.BAFsegmentation


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Timestamp:
Dec 12, 2011, 10:41:20 AM (7 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v38 v39  
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    77=== News ===
     8
     9 * Dec. 12, 2011. We are currently working on BAFsegmentation 2.0, in which the main aim is improving results for noisier samples and samples with high purity (e.g. cell lines). We have published a new paper, Staaf et al. Breast Cancer Research, 2011 "Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer", for which we have made a pre-release with 2.0 functionality available: [#pre-release BAFsegmentation 2.0pre]. 
    810
    911 * Jun. 1, 2010. BAFsegmentation 1.2.0 release. Added support for analysing paired tumor-normal samples.
     
    146148    * A file with a plot for each chromosome of regions of allelic imbalance across all assays.
    147149
     150=== BAFsegmentation 2.0 pre-release #pre-release
     151
     152This version of the BAF segmentation software corresponds to the version used in Staaf et al. Breast Cancer Research, 2011 "Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer". The main change in this version compared to earlier versions is that a double segmentation is performed aimed at improving results for noisier samples and samples with high purity (e.g. cell lines). This version requires different input formats and some additional variables compared to 1.x versions. Notably, the data needs to be pre-compiled using R into RData objects as described in the zip-file. This version works on a per data set basis, allowing multiple data sets to be specified with different parameters. We are planning to integrate this new version into the same frame-work as older versions, with potential additional changes to improve performance, and release it as BAFsegmentation 2.0.
     153
     154[http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/BAFsegmentation-2.0pre-snapshot111209.zip?format=raw Download the 2.0 pre-release (BAFsegmentation 2.0pre-snapshot111209).]
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     156
    148157=== Contact ===
    149158