18 skills found
AmpliconSuite / AmpliconSuite PipelineA quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes AmpliconClassifier
iprada / Circle MapA method for circular DNA detection based on probabilistic mapping of ultrashort reads
nf-core / CircdnaPipeline 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.
AmpliconSuite / AmpliconClassifierClassify output of AmpliconArchitect to detect types of focal amplifications present
ShixiangWang / GcapGCAP (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
AmpliconSuite / AmpliconReconstructorOMReconstructs complex variation using Bionano optical mapping data and breakpoint graph data
UCRajkumar / EcSegTool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.
madagiurgiu25 / Decoil PreReconstruct ecDNA from long-read data using Decoil tool
sssimonyang / EcDNA FinderA new software to calculate ecDNA from WGS bam file.
XSLiuLab / EcDNA ImmuneExtrachromosomal DNA is associated with decreased immune cell infiltration and antigen presentation, represents a potential cancer immune evasion mechanism
pierrj / Ecc Callerecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.
HuMingLab / EcDNAcallerNo description available
madagiurgiu25 / Decoil VizVisualize circular ecDNA reconstructions using Decoil-viz
suda-huanglab / CirclehunterA pipeline for identifying complex ecDNA using ATAC-Seq data.
chenlab2019 / EcDNA On GCAExtrachromosomal DNA is associated with the chromothripsis and the diverse patient prognosis in the gastric cardia adenocarcinoma
ChangLab / EcDNA Hub Code 2021Code for Hung*, Yost*, Xie*, et al. ecDNA hubs drive cooperative intermolecular oncogene expression (2021).
AmpliconSuite / AmpliconRepositoryWebsite to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
snakemake-workflows / Cyrcular CallingA Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
