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.

Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 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.

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

Landing page for my github!

Cell-free DNA fragmentation analysis directly from electrophoresis data

A 3-stage ML cascade for non-invasive Alzheimer's risk stratification using plasma biomarkers (ADNI data) — includes a local web screening interface.

Liver Lipidomics Paper