Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeBuilder

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    File d= new File(dir+"/other_datasets/lee_2007");
   
    File f= new File(d+"/analyzed_data_complete_bw20.bar");
   
    BarReader br= new BarReader(f);
    LandscapeBuilder lb= br.getLandscapeBuilder();
   
    new LandscapeTransformer(lb).unlog();
   
    new BarExporter(lb, br.header()).writeToFile(new File(d+"/unlog_"+f.getName()));
   
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        String samp= samps[i];
       
        File ff= new File(datd+"/strand_rna_"+samp+"_sacCer1_for.wig");
        File rf= new File(datd+"/strand_rna_"+samp+"_sacCer1_rev.wig");
       
        LandscapeBuilder lbf= new BedGraphReader(ff).getLandscapeBuilder();
        LandscapeBuilder lbr= new BedGraphReader(rf).getLandscapeBuilder();
       
        NormRNASeq nn= new NormRNASeq(lbf, lbr, gb);
        nn.writeToFiles(
                new File(od+"/norm_"+ff.getName()),
                new File(od+"/norm_"+rf.getName())
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Related Classes of fork.lib.bio.anno.genomic.LandscapeBuilder

  • data.cerevisiae.at.Score
  • data.cerevisiae.auerbach2013_polii.Score
  • data.cerevisiae.ConsToWig
  • data.cerevisiae.histmod.cai2011.Score
  • data.cerevisiae.histmod.cai2011.ToWig
  • data.cerevisiae.histmod.guillemett2011_h3k4.Unlog
  • data.cerevisiae.histmod.guillemette2011.Score
  • data.cerevisiae.histmod.guillemette2011.ToWig
  • data.cerevisiae.histmod.kirmizis2009.Score
  • data.cerevisiae.histmod.liu2005_histmods.LineupThree
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