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

Identification of gene-fusions, including EML4-ALK

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

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

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.

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

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

Extract read counts from cfDNA

Landing page for my github!

Cell-free DNA fragmentation analysis directly from electrophoresis data

Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

PSTquant quantifies a patient's ctDNA levels by creating a patient-specific reference and counting the fusion and wild-type supporting reads.

Liver Lipidomics Paper

Analysis of sequencing coverage bias in cfDNA relative to matched tumor data from targeted sequencing.