AmpliconSuite

All

15 repositories

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.
cancer cancer-genomics ecdna
Python
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Other
•28•62•21•0•Updated Feb 11, 2025Feb 11, 2025
AmpliconRepository
Public
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
cancer genomics-data bfb ecdna
JavaScript
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BSD 3-Clause "New" or "Revised" License
•5•1•12•0•Updated Feb 10, 2025Feb 10, 2025
CoRAL
Public
Reconstruction of focal amplifications with long reads
Python
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BSD 3-Clause "New" or "Revised" License
•4•18•8•2•Updated Feb 6, 2025Feb 6, 2025
ec3D
Public
Reconstruct the three-dimensional structure of extrachromosomal DNA
Python
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BSD 3-Clause "New" or "Revised" License
•0•4•0•0•Updated Feb 3, 2025Feb 3, 2025
AmpliconClassifier
Public
Classify output of AmpliconArchitect to detect types of focal amplifications present
focal double-minutes bfb ecdna ampliconarchitect python-library amplicons
Python
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BSD 2-Clause "Simplified" License
•11•18•11•0•Updated Jan 30, 2025Jan 30, 2025
ecSimulator
Public
Simulate ecDNA structures with user-specified properties.
bioinformatics genome simulation cancer-genomics structural-variation ecdna
Python
•3•0•0•0•Updated Jan 27, 2025Jan 27, 2025
CycleViz
Public
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
Python
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GNU General Public License v3.0
•6•24•2•0•Updated Jan 15, 2025Jan 15, 2025
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.4k•0•0•0•Updated Dec 12, 2024Dec 12, 2024
AmpliconArchitect
Public
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
bioinformatics cancer copynumber ecdna
Python
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Other
•43•9•0•0•Updated Dec 12, 2024Dec 12, 2024
AmpliconSuiteAggregator
Public
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
Python
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Other
•4•2•2•0•Updated Dec 5, 2024Dec 5, 2024
CRISPRCATCH
Public
Pipeline for reconstructing ecDNA based on data from PFGE
Python
•1•0•0•0•Updated Aug 19, 2024Aug 19, 2024
.github
Public
Organization documentation
0•0•0•0•Updated Apr 26, 2024Apr 26, 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
AmpliconRepository-docs
Public
0•0•0•0•Updated Dec 11, 2023Dec 11, 2023
AmpliconReconstructorOM
Public
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
cancer-genomics genome-sequencing genome-analysis genome-assembly optical-mapping bionano ecdna python ngs
Python
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Other
•6•16•4•0•Updated Nov 13, 2023Nov 13, 2023