Changes between Version 39 and Version 40 of se.lu.onk.BAFsegmentation


Ignore:
Timestamp:
May 31, 2021, 2:10:23 PM (3 weeks ago)
Author:
Jari Häkkinen
Comment:

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  • se.lu.onk.BAFsegmentation

    v39 v40  
    3333=== Download BAFsegmentation ===
    3434
    35 [http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/BAFsegmentation-1.2.0.zip?format=raw Download the latest stand-alone release (BAFsegmentation 1.2.0).]
     35[attachment:BAFsegmentation-1.2.0.zip?format=raw Download the latest stand-alone release (BAFsegmentation 1.2.0).]
    3636
    3737=== Supplemental Data ===
    3838
    39  * The plots referred to in additional data file 4 in the manuscript are available [http://cbbp.thep.lu.se/~markus/publications/papers/BAFsegmentation_supplemental_data.zip here].
    40  * The simulated data set used in the publication is available [http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/SimulatedTumorData.zip?format=raw here].
     39 * The simulated data set used in the publication is available [attachment:SimulatedTumorData.zip?format=raw here].
    4140 * Infinium data for four matched tumor-normal pairs and a dilution series of a tumor cell line mixed with its paired normal cell line are available in NCBI's Gene Expression Omnibus with accession [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976 GSE11976].
    42  * The Infinium data for the dilution series of a tumor cell line mixed with its paired normal cell line are also available as a [http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/CRL2324_dilutionSeries_BeadStudio.zip?format=raw BeadStudio project] and as a [http://cbbp.thep.lu.se/~markus/software/BAFsegmentation/CRL2324_dilutionSeries_TableExport.zip?format=raw tab-delimited text file] exported from Beadstudio.
     41 * The Infinium data for the dilution series of a tumor cell line mixed with its paired normal cell line are also available as a [attachment:CRL2324_dilutionSeries_BeadStudio.zip?format=raw BeadStudio project] and as a [attachment:CRL2324_dilutionSeries_TableExport.zip?format=raw tab-delimited text file] exported from Beadstudio.
    4342
    4443=== How to use BAFsegmentation ===
     
    152151This 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.
    153152
    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).]
     153[attachment:BAFsegmentation-2.0pre-snapshot111209.zip?format=raw Download the 2.0 pre-release (BAFsegmentation 2.0pre-snapshot111209).]
    155154
    156155