cfdna

There are 0 repository under cfdna topic.

• XWangLabTHU / cfDNApipe

  cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

  cell-free-dnacfdnawgs-datawgbs-datasnvvirus-detectioncnv
  Language:Python 59

• OpenGene / CfdnaPattern

  Pattern Recognition for Cell-free DNA

  bioinformaticscfdnangspattern
  Language:Python 58

• alkodsi / ctDNAtools

  R package to work with ctDNA sequencing data

  ctdnacfdnacancergenomicsliquid-biopsysequencingmutationsngscirculating-tumor-dnacell-free-dnamrd
  Language:R 35

• christacaggiano / celfie

  cfDNA cell type of origin estimation

  cfdna
  Language:Jupyter Notebook 29

• ndbrown6 / MSK-GRAIL-TECHVAL

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

  rcancercfdnactdnaclonal-hematopoiesiscopy-number
  Language:R 21

• christacaggiano / cell-free-dna-reading-list

  Important papers relating to the biology of cell free DNA

  cfdnadeconvolutionmethylation
  18

• epifluidlab / FinaleToolkit

  FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

  bioinformaticsbioinformatics-toolcell-free-dnacfdnacomputational-biologyepigenomicsfragmentomicsgenomicsgenomics-analysis
  Language:Python 12

• Isy89 / LBF

  bioinformaticsbiomarker-discoverycfdnaclidifferential-transcription-factors-activityfeature-extractionfragmentomicsliquid-biopsyplugin-systempython3transcription-factor-binding-sitetranscription-factorstranscription-start-sitetui
  Language:Python 10

• pburnham50 / LowBiomassBackgroundCorrection

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

  cfdnadiagnosticsmicrobial-genomes
  Language:Roff 8

• christacaggiano / mybaits-probe-design

  cfDNA methylation probe design from mybaits targeted sequencing

  cfdnamethylationprobe-design
  Language:Python 4

• 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.

  bioinformaticscell-free-dnacfdnaclassificationctdnadeconvolutionfeature-selectionfractional-phenotype-estimationwgswhole-genome-sequencing
  Language:Python 3

• nickveltmaat / SNVcaller

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

  somatic-variantssomatic-mutationssnvssnvsnv-annotationcell-free-dnactdnacfdnalofreqmutect2vardictsinvictindel
  Language:Python 3

• TobiasRoikjer / NucCa

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

  nucleosomescancer-researchctdnacfdna
  Language:C 2

• msk-access / nucleo_qc

  Quality Control Workflow for UMI based BAMs

  cfdnachip
  Language:Common Workflow Language 1

• ndbrown6 / MSK-BYL-NC

  Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors

  rcfdnacancer
  Language:R 1

• benloklab / cfmedip_sclc_iscience

  This repository contains the code used in the following publication: doi.org/10.1016/j.isci.2022.105487

  cfdnadna-methylationepigeneticsliquid-biopsysmall-cell-lung-cancer
  Language:R 0

• benloklab / sclc_cfmedip_PRIME

  Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 10.1016/j.isci.2022.105487

  cfdnaepigeneticsfiltering-algorithmliquid-biopsysclc
  Language:R 0

• christacaggiano / lung_transplant_cfdna

  code for lung transplant cfdna project

  cfdnamethylation
  Language:R

• CTLife / cfDNA-5hmC_LungCancer

  Plasma cell-free DNA hydroxymethylomes discriminate disease state in EGFR-mutant non-small cell lung cancer.

  cfdna5hmcbioinformaticsliquid-biopsylung-cancerpredictiondisease-stateheterogeneitymachine-learning-modelnon-small-cell-lung-cancernsclcegfr-mutant
  Language:R

• drvenki / sv-cfdna

  Structural Variants in cell-free tumor DNA

  liquidbiosycfdnacellfreednacellfreectdnacirculatingtumordnastructural-variationstructural-variantscf-dnact-dnacell-free-dnacirculating-tumor

• msk-access / uncollapsed_bam_generation

  Workflow for making MSK-ACCESS standard binary alignment mapping file.

  cfdnactdnacwlcwl-workflowumiworkflow
  Language:Common Workflow Language