Table A1:
Open in new tab

Software for preprocessing aCGH profiles

ReferenceSourceNamePlatform
Removing wave-like artifacts
Diskin et al. [8]http://www.openbioinformatics.org/penncnv/PennCNV-gcmodelStand-alone
Van de Wiel et al. [9]http://www.few.vu.nl/∼mavdwiel/nowaves.htmlNoWavesR
Normalization
Staaf et al. [10]CRANpopLowessR
Chen et al. [11]http://ntumaps.cgm.ntu.edu.tw/aCGH supplementary/Matlab
Segmentation, smoothing and calling
Marioni et al. [12]BioconductorsnapCGHR
Rueda et al. [14]CRANRJaCGHR
Olshen et al. [15]BioconductorDNAcopyR
Rancoita et al. [16]http://www.idsia.ch/∼paola/mBPCR/mBPCRR
Huang et al. [17]http://www.meb.ki.se/∼yudpaw/smoothsegR
Van de Wiel et al. [21]BioconductorCGHcallR
Picard et al. [22]CRANsegclustR/C++
Pique-Regi et al. [25]http://biron.usc.edu/∼piquereg/GADA/GADA.htmlGADAStand-alone
Díaz-Uriarte et al. [26]http://adacgh.bioinfo.cnio.es/ & CRANadaCGHStand-alone & R
ReferenceSourceNamePlatform
Removing wave-like artifacts
Diskin et al. [8]http://www.openbioinformatics.org/penncnv/PennCNV-gcmodelStand-alone
Van de Wiel et al. [9]http://www.few.vu.nl/∼mavdwiel/nowaves.htmlNoWavesR
Normalization
Staaf et al. [10]CRANpopLowessR
Chen et al. [11]http://ntumaps.cgm.ntu.edu.tw/aCGH supplementary/Matlab
Segmentation, smoothing and calling
Marioni et al. [12]BioconductorsnapCGHR
Rueda et al. [14]CRANRJaCGHR
Olshen et al. [15]BioconductorDNAcopyR
Rancoita et al. [16]http://www.idsia.ch/∼paola/mBPCR/mBPCRR
Huang et al. [17]http://www.meb.ki.se/∼yudpaw/smoothsegR
Van de Wiel et al. [21]BioconductorCGHcallR
Picard et al. [22]CRANsegclustR/C++
Pique-Regi et al. [25]http://biron.usc.edu/∼piquereg/GADA/GADA.htmlGADAStand-alone
Díaz-Uriarte et al. [26]http://adacgh.bioinfo.cnio.es/ & CRANadaCGHStand-alone & R
Table A1:
Open in new tab

Software for preprocessing aCGH profiles

ReferenceSourceNamePlatform
Removing wave-like artifacts
Diskin et al. [8]http://www.openbioinformatics.org/penncnv/PennCNV-gcmodelStand-alone
Van de Wiel et al. [9]http://www.few.vu.nl/∼mavdwiel/nowaves.htmlNoWavesR
Normalization
Staaf et al. [10]CRANpopLowessR
Chen et al. [11]http://ntumaps.cgm.ntu.edu.tw/aCGH supplementary/Matlab
Segmentation, smoothing and calling
Marioni et al. [12]BioconductorsnapCGHR
Rueda et al. [14]CRANRJaCGHR
Olshen et al. [15]BioconductorDNAcopyR
Rancoita et al. [16]http://www.idsia.ch/∼paola/mBPCR/mBPCRR
Huang et al. [17]http://www.meb.ki.se/∼yudpaw/smoothsegR
Van de Wiel et al. [21]BioconductorCGHcallR
Picard et al. [22]CRANsegclustR/C++
Pique-Regi et al. [25]http://biron.usc.edu/∼piquereg/GADA/GADA.htmlGADAStand-alone
Díaz-Uriarte et al. [26]http://adacgh.bioinfo.cnio.es/ & CRANadaCGHStand-alone & R
ReferenceSourceNamePlatform
Removing wave-like artifacts
Diskin et al. [8]http://www.openbioinformatics.org/penncnv/PennCNV-gcmodelStand-alone
Van de Wiel et al. [9]http://www.few.vu.nl/∼mavdwiel/nowaves.htmlNoWavesR
Normalization
Staaf et al. [10]CRANpopLowessR
Chen et al. [11]http://ntumaps.cgm.ntu.edu.tw/aCGH supplementary/Matlab
Segmentation, smoothing and calling
Marioni et al. [12]BioconductorsnapCGHR
Rueda et al. [14]CRANRJaCGHR
Olshen et al. [15]BioconductorDNAcopyR
Rancoita et al. [16]http://www.idsia.ch/∼paola/mBPCR/mBPCRR
Huang et al. [17]http://www.meb.ki.se/∼yudpaw/smoothsegR
Van de Wiel et al. [21]BioconductorCGHcallR
Picard et al. [22]CRANsegclustR/C++
Pique-Regi et al. [25]http://biron.usc.edu/∼piquereg/GADA/GADA.htmlGADAStand-alone
Díaz-Uriarte et al. [26]http://adacgh.bioinfo.cnio.es/ & CRANadaCGHStand-alone & R
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