ecdna

There are 16 repositories under ecdna topic.

  • iprada/Circle-Map

    A method for circular DNA detection based on probabilistic mapping of ultrashort reads

    Language:Python6268320

  • 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.

    Language:Python5365728

  • nf-core/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.

    Language:Python281512314

  • AmpliconSuite/AmpliconReconstructorOM

    Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data

    Language:Python15366

  • ShixiangWang/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-universe.dev/gcap

    Language:R153462

  • UCRajkumar/ecSeg

    Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.

    Language:Python15119

  • AmpliconSuite/AmpliconClassifier

    Classify output of AmpliconArchitect to detect types of focal amplifications present

    Language:Python1451811

  • AmpliconSuite/AmpliconArchitect

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

    Language:Python85011

  • pierrj/ecc_caller

    ecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.

    Language:Python6113

  • madagiurgiu25/decoil-viz

    Visualize circular ecDNA reconstructions using Decoil-viz

    Language:Python2130

  • AmpliconSuite/AmpliconRepository

    Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.

    Language:JavaScript141575

  • genepattern/AmpliconSuite

    Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

    Language:Python1201

  • henssen-lab/decoil-paper

    Scripts and analysis for the Giurgiu et al. 2024. Genome Research. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".

    Language:Jupyter Notebook1101

  • AmpliconSuite/ecSimulator

    Simulate ecDNA structures with user-specified properties.

    Language:Python0303

  • fraterenz/ecdna-evo

    Evolutionary models of extrachromosomal DNA (ecDNA).

    Language:Rust01770

  • madagiurgiu25/ecDNA-sim

    Simulation of ecDNA sequence templates

    Language:Python0100