ctdna 开源项目推荐（30 个）

nf-core /oncoanalyser

全面的癌症DNA/RNA分析和报告管道

alkodsi /ctDNAtools

R package to work with ctDNA sequencing data

OpenGene /ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

ndbrown6 /MSK-GRAIL-TECHVAL

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

mikessh /mageri

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

ctDNA /TNER

TNER: Tri-Nucleotide Error Reducer for ctDNA detection

reiterlab /ctdna

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

OpenGene /dedup

Deduplication for cfDNA sequencing data

odinokov /cfdna-tools

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

denniepatton /Keraon

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.

HaoKuo /ctCNV

A new CNV calling method for DNA-seq data

dkleftogi /duplexFiltering

duplex DNA molecule identification tool for ultra-sensitive SNV detection

gaarangoa /MetaCH

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

TobiasRoikjer /NucCa

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

dkleftogi /AmpliSolve

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

Green-Lab-MDACC /lpWGS_pipeline

该项目在 GitHub 上没有填写描述

msk-access /bam_collapsing

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

denniepatton /Triton

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.

bdolmo /fragment_extractor

Extract read counts from cfDNA

Green-Lab-MDACC /CAPP_SEQ_pipeline

该项目在 GitHub 上没有填写描述