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1. AmpliconSuite/AmpliconSuite-pipeline AmpliconSuite/AmpliconSuite-pipeline Public

   A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

   Python 56 28

2. AmpliconSuite/CycleViz AmpliconSuite/CycleViz Public

   Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.

   Python 24 6

3. ReactionDiffusionSimulator ReactionDiffusionSimulator Public

   Simulate and visualize reaction-diffusion models and Turing patterns

   Python 19 1

4. AmpliconSuite/AmpliconClassifier AmpliconSuite/AmpliconClassifier Public

   Classify output of AmpliconArchitect to detect types of focal amplifications present

   Python 16 11

5. AmpliconSuite/CoRAL AmpliconSuite/CoRAL Public

   Reconstruction of focal amplifications with long reads

   Python 12 3

6. AmpliconSuite/AmpliconArchitect AmpliconSuite/AmpliconArchitect Public

   Forked from virajbdeshpande/AmpliconArchitect

   Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.

   Python 8 11