cfdna

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

bioinformatics genomics cpp ngs variant-calling cfdna nipt basevar

UpdatedMar 6, 2025
C

ndbrown6 /MSK-GRAIL-TECHVAL

Star22

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

r cancer ctdna copy-number cfdna clonal-hematopoiesis

UpdatedMar 27, 2020
R

epifluidlab /FinaleToolkit

Star21

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

UpdatedMar 12, 2025
Python

christacaggiano /cell-free-dna-reading-list

Star19

Important papers relating to the biology of cell free DNA

methylation deconvolution cfdna

UpdatedSep 21, 2018

Isy89 /LBF

Star11

cli bioinformatics transcription-factors tui python3 feature-extraction plugin-system biomarker-discovery cfdna liquid-biopsy transcription-factor-binding-site fragmentomics transcription-start-site differential-transcription-factors-activity

UpdatedSep 30, 2024
Python

pburnham50 /LowBiomassBackgroundCorrection

Star9

R package and vignette to denoise metagenomic cell-free DNA sequencing data.

diagnostics microbial-genomes cfdna

UpdatedNov 5, 2019
Roff

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

UpdatedJun 6, 2024
Python

BesenbacherLab /lionheart

Star4

LIONHEART is a method for detecting cancer from whole genome sequenced plasma cell-free DNA.

cancer-genomics whole-genome-sequencing cfdna cancer-detection cell-free-dna chromatin-accessibiity fragmentomics

UpdatedMar 2, 2025
Python

christacaggiano /mybaits-probe-design

Star4

cfDNA methylation probe design from mybaits targeted sequencing

methylation cfdna probe-design

UpdatedJul 13, 2018
Python

nickveltmaat /SNVcaller

Star3

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

somatic-variants somatic-mutations snv ctdna snvs cfdna vardict mutect2 cell-free-dna snv-annotation indel lofreq sinvict

UpdatedNov 8, 2022
Python

zhuhuanhuan20220519 /cfGWAS

Star2

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.

cfdna