cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
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Aug 18, 2022 - Python
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cfdna
Here are 38 public repositories matching this topic...
R package to work with ctDNA sequencing data
genomics cancer ngs sequencing mutations ctdna cfdna liquid-biopsy cell-free-dna mrd circulating-tumor-dna
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Feb 20, 2022 - R
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
bioinformatics genomics computational-biology cfdna epigenomics cell-free-dna bioinformatics-tool fragmentomics genomics-analysis
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Oct 1, 2025 - Python
This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data
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Jul 28, 2025 - C
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
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Mar 27, 2020 - R
Important papers relating to the biology of cell free DNA
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Sep 21, 2018
R package and vignette to denoise metagenomic cell-free DNA sequencing data.
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Nov 5, 2019 - Roff
LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.
cancer-genomics whole-genome-sequencing cfdna cancer-detection cell-free-dna chromatin-accessibiity fragmentomics
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Sep 9, 2025 - Python
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.
bioinformatics feature-selection classification wgs ctdna deconvolution whole-genome-sequencing cfdna cell-free-dna fractional-phenotype-estimation
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Aug 28, 2025 - Python
This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data
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Sep 22, 2025 - C
cfDNA methylation probe design from mybaits targeted sequencing
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Jul 13, 2018 - Python
This repository serves as a dedicated space for housing the codebase used in our publication for cfGWAS reveal genetic basis of cell-free DNA features. It is intended to provide researchers with access to the methodologies and algorithms employed in our study, facilitating further research and analysis in the field of genetic.
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Nov 7, 2024 - R
Cancer estimation based on nucleosomes: Analysis of proportion of circulating tumor DNA fragments compared to nucleosome references.
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Dec 2, 2019 - C
Plasma cell-free DNA hydroxymethylomes discriminate disease state in EGFR-mutant non-small cell lung cancer.
bioinformatics prediction lung-cancer cfdna heterogeneity liquid-biopsy machine-learning-model non-small-cell-lung-cancer nsclc 5hmc disease-state egfr-mutant
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Mar 17, 2023 - R
Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 10.1016/j.isci.2022.105487
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Aug 28, 2023 - R
Integrative analysis of cfDNA methylation and miRNA expression for early lung cancer detection using machine learning.
machine-learning bioinformatics genomics methylation lung-cancer-detection mirna cfdna cancer-detection liquid-biopsy healthcare-ai
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Aug 11, 2025 - Jupyter Notebook
This repository contains the code used in the following publication: doi.org/10.1016/j.isci.2022.105487
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Jun 27, 2023 - R
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