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  "Title": "Joint Peak Detection in Several ChIP-Seq Samples",
  "Description": "Jointly segment several ChIP-seq samples to find the peaks\nwhich are the same and different across samples. The fast\napproximate maximum Poisson likelihood algorithm is described\nin \"PeakSegJoint: fast supervised peak detection via joint\nsegmentation of multiple count data samples\"\n<doi:10.48550/arXiv.1506.01286> by TD Hocking and G Bourque.",
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    "PeakSegJointHeuristicStep2",
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