cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
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Updated
Aug 18, 2022 - Python
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cell-free-dna
Here are 8 public repositories matching this topic...
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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Jan 15, 2025 - Python
Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.
bioinformatics genomics ngs sequencing dna variant-calling fetal cell-free-dna nipt cell-free-fetal-dna
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Jun 5, 2019 - Python
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
quality-control annotation chip-seq atac-seq bulk cell-free-dna peak-calling differential-accessibility differential-binding
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Jan 13, 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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Jun 6, 2024 - Python
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
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Nov 8, 2022 - Python
cell-free ChIP-seq pipeline
quality-control snakemake chip-seq cell-free-dna peak-calling peak-annotation cell-type-deconvolution
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Feb 7, 2024 - Python
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
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Jan 9, 2025 - Python
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