R package to work with ctDNA sequencing data

cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

A simplified pipeline for ctDNA sequencing data analysis

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

A framework for learning low dimensional representations of single-cell images, here applied in enrichment-free liquid biopsies

Identification of gene-fusions, including EML4-ALK

Simple scripts to parallelize miRNA analysis with sRNAtoolbox performed for my Master thesis.

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

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

Extract read counts from cfDNA

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

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

Landing page for my github!

Cell-free DNA fragmentation analysis directly from electrophoresis data