Pinned Repositories
.github
Organization documentation
AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
AmpliconClassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
AmpliconRepository
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
AmpliconRepository-docs
AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
CoRAL
Reconstruction of focal amplifications with long reads
CycleViz
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
AmpliconSuite's Repositories
AmpliconSuite/AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
AmpliconSuite/CycleViz
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
AmpliconSuite/AmpliconClassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
AmpliconSuite/AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
AmpliconSuite/CoRAL
Reconstruction of focal amplifications with long reads
AmpliconSuite/AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
AmpliconSuite/AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
AmpliconSuite/AmpliconRepository
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
AmpliconSuite/.github
Organization documentation
AmpliconSuite/AmpliconRepository-docs
AmpliconSuite/bioconda-recipes
Conda recipes for the bioconda channel.
AmpliconSuite/ecSimulator
Simulate ecDNA structures with user-specified properties.
AmpliconSuite/CRISPRCATCH
Pipeline for reconstructing ecDNA based on data from PFGE
AmpliconSuite/GenePatternFileDownloader
Utility script for downloading bam (or other file types) from GenePattern