cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Pattern Recognition for Cell-free DNA

R package to work with ctDNA sequencing data

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

cfDNA cell type of origin estimation

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

Important papers relating to the biology of cell free DNA

No description provided.

LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.

R package and vignette to denoise metagenomic cell-free DNA sequencing data.

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT 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.

cfDNA methylation probe design from mybaits targeted sequencing

This repository serves as a dedicated space for housing the codebase used in our publication for cfGWAS reveal genetic basis of cell-free DNA features. It is intended to provide researchers with access to the methodologies and algorithms employed in our study, facilitating further research and analysis in the field of genetic.

Cancer estimation based on nucleosomes: Analysis of proportion of circulating tumor DNA fragments compared to nucleosome references.

A flexible and sensitive method for capturing and integrating multimodal epigenetic information from cell-free DNA (cfDNA) using a single experimental assay.

This repository contains the code used in the following publication: doi.org/10.1016/j.isci.2022.105487

Integrative analysis of cfDNA methylation and miRNA expression for early lung cancer detection using machine learning.

Plasma cell-free DNA hydroxymethylomes discriminate disease state in EGFR-mutant non-small cell lung cancer.

Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 10.1016/j.isci.2022.105487

Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors

An integrated deconvolution approach to cfDNA methylation data.

Quality Control Workflow for UMI based BAMs

Extract read counts from cfDNA

As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions and outputs both region-level biomarkers and nt-resolution signal profiles.

Structural Variants in cell-free tumor DNA

CEliver model

Raw signals were basecalled with Dorado and aligned to hg38.p13 using minimap2. Tumor fraction and CNVs were estimated with HMMcopy and ichorCNA. Motif analysis extracted the first four 5′ nucleotides per read, and NMF identified three dominant motif profiles capturing key variability among samples.

code for lung transplant cfdna project