ecdna topic
Circle-Map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
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.
circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
ecSeg
Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.
gcap
GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data and absolute copy number profiles. https://shixiangwang.r-univer...