cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
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Updated
Aug 18, 2022 - Python
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
R package to work with ctDNA sequencing data
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
Important papers relating to the biology of cell free DNA
R package and vignette to denoise metagenomic cell-free DNA sequencing data.
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.
Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 10.1016/j.isci.2022.105487
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
This repository contains the code used in the following publication: doi.org/10.1016/j.isci.2022.105487
cfDNA methylation probe design from mybaits targeted sequencing
Plasma cell-free DNA hydroxymethylomes discriminate disease state in EGFR-mutant non-small cell lung cancer.
Cancer estimation based on nucleosomes: Analysis of proportion of circulating tumor DNA fragments compared to nucleosome references.
Structural Variants in cell-free tumor DNA
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