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    19 repositories

    • AmpliconRepository

      Public
      Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
      cancergenomics-databfb
      cancergenomics-databfbecdna
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •5•6•15•0•Updated Sep 2, 2026Sep 2, 2026

    • ec3D

      Public
      Reconstruct the three-dimensional structure of extrachromosomal DNA
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•0•1•Updated Sep 2, 2026Sep 2, 2026

    • CoRAL

      Public
      CoRAL: Reconstruction of focal amplifications with long reads
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•31•18•1•Updated Aug 22, 2026Aug 22, 2026

    • AmpliconRepository-docs

      Public
      0•0•0•0•Updated Aug 21, 2026Aug 21, 2026

    • CycleExtractor

      Public
      Python
      •1•5•1•0•Updated Aug 19, 2026Aug 19, 2026

    • AmpliconSuiteAggregator

      Public
      Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
      Python
      •
      Other
      •4•3•3•0•Updated Aug 17, 2026Aug 17, 2026

    • EC-comparator

      Public
      Compare amplicon sets across technologies and methods
      Python
      •0•1•0•0•Updated Aug 12, 2026Aug 12, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4.1k•0•0•0•Updated Jul 29, 2026Jul 29, 2026

    • AmpliconSuite-pipeline

      Public
      A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes Amp…
      cancercancer-genomicsecdna
      cancercancer-genomicsecdna
      Python
      •
      Other
      •33•87•35•0•Updated Jul 23, 2026Jul 23, 2026

    • BFBArchitect

      Public
      A tool for reconstructing breakage fusion bridge amplifications from whole genome sequencing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Jul 23, 2026Jul 23, 2026

    • AmpliconArchitect

      Public
      Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
      bioinformaticscancercopynumber
      bioinformaticscancercopynumberecdna
      Python
      •
      Other
      •45•13•0•0•Updated Jul 22, 2026Jul 22, 2026

    • AmpliconClassifier

      Public
      Classify output of AmpliconArchitect to detect types of focal amplifications present
      python-libraryampliconsfocal
      python-libraryampliconsfocaldouble-minutesbfbecdnaampliconarchitect
      Python
      •
      BSD 2-Clause "Simplified" License
      •12•23•16•0•Updated Jul 22, 2026Jul 22, 2026

    • .github

      Public
      Organization documentation
      0•0•0•0•Updated Jul 1, 2026Jul 1, 2026

    • AmpliconSuite-docs

      Public
      Shared documentation for AmpliconSuite file formats and conventions
      0•0•0•0•Updated May 19, 2026May 19, 2026

    • ecSimulator

      Public
      Simulate ecDNA structures with user-specified properties.
      bioinformaticsgenomesimulation
      bioinformaticsgenomesimulationcancer-genomicsstructural-variationecdna
      Python
      •4•6•0•0•Updated Feb 10, 2026Feb 10, 2026

    • CycleViz

      Public
      Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
      Python
      •
      GNU General Public License v3.0
      •6•30•4•0•Updated Oct 10, 2025Oct 10, 2025

    • CRISPRCATCH

      Public
      Pipeline for reconstructing ecDNA based on data from PFGE
      Python
      •1•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • GenePatternFileDownloader

      Public
      Utility script for downloading bam (or other file types) from GenePattern
      Python
      •0•0•0•0•Updated Jan 12, 2024Jan 12, 2024

    • AmpliconReconstructorOM

      Public
      Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
      pythonngscancer-genomics
      pythonngscancer-genomicsgenome-sequencinggenome-analysisgenome-assemblyoptical-mappingbionanoecdna
      Python
      •
      Other
      •6•19•5•0•Updated Nov 13, 2023Nov 13, 2023
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