ctdna

A comprehensive cancer DNA/RNA analysis and reporting pipeline

R package to work with ctDNA sequencing data

A simplified pipeline for ctDNA sequencing data analysis

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

[DEPRECATED] MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

TNER: Tri-Nucleotide Error Reducer for ctDNA detection

Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding

Deduplication for cfDNA sequencing data

A searchable catalog of cfDNA tools for WGS, methylation, CNA, end motif, coverage, and tissue-origin workflows.

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.

A new CNV calling method for DNA-seq data

duplex DNA molecule identification tool for ultra-sensitive SNV detection

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

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

Prediction of clonal hematopoiesis (CH) variants in cfDNA using machine learning. Includes pretrained models, example inference notebook, and reproducible analysis code.

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

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.

Intra-treatment ctDNA and imaging dynamics identify candidates for adaptive therapy in HPV-related oropharyngeal cancer