R package to work with ctDNA sequencing data
A simplified pipeline for ctDNA sequencing data analysis
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
Deduplication for cfDNA sequencing data
Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding
As a tool for cancer subtype prediction, Keraon uses features derived from cell-free DNA (cfDNA) in conjunction with PDX reference models to perform both classification and heterogenous phenotype fraction estimation.
duplex DNA molecule identification tool for ultra-sensitive SNV detection
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
Identification of single nucleotide variants using position-specific error estimation in deep sequencing data
Cancer estimation based on nucleosomes: Analysis of proportion of circulating tumor DNA fragments compared to nucleosome references.
Supplementary files for Paracchini, Beltrame et al., Clin Cancer Res, 2020.
Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS
Structural Variants in cell-free tumor DNA
Extract read counts from cfDNA
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