ctdna

There are 1 repository under ctdna topic.

• OpenGene / ctdna-pipeline

  A simplified pipeline for ctDNA sequencing data analysis

  ctdnaliquid-biopsyngspipelinebioinformatics
  Language:Shell 36

• alkodsi / ctDNAtools

  R package to work with ctDNA sequencing data

  ctdnacfdnacancergenomicsliquid-biopsysequencingmutationsngscirculating-tumor-dnacell-free-dnamrd
  Language:R 34

• ctDNA / TNER

  TNER: Tri-Nucleotide Error Reducer for ctDNA detection

  ctdna
  Language:R 21

• mikessh / mageri

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

  bioinformaticscancerumivariantmutationmappingampliconexonctdna
  Language:Java 21

• ndbrown6 / MSK-GRAIL-TECHVAL

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

  rcancercfdnactdnaclonal-hematopoiesiscopy-number
  Language:R 21

• OpenGene / dedup

  Deduplication for cfDNA sequencing data

  ngsctdnaliquiddeduplicationbioinformatics
  Language:Python 10

• reiterlab / ctdna

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

  cancerctdnagenomicscancer-evolutionliquid-biopsies
  Language:Python 10

• HaoKuo / ctCNV

  A new CNV calling method for DNA-seq data

  cnvctdna
  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-selectionwgswhole-genome-sequencingfractional-phenotype-estimation
  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

• Green-Lab-MDACC / lpWGS_pipeline

  low-coverage-sequencingcell-free-dnactdnapaired-end-sequencingpaired-end-fastq-trimming
  Language:C 2

• TobiasRoikjer / NucCa

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

  nucleosomescancer-researchctdnacfdna
  Language:C 2

• lbeltrame / mnegri-ov264

  Supplementary files for Paracchini, Beltrame et al., Clin Cancer Res, 2020.

  bioinformaticscancerctdna
  Language:Nextflow 1

• Green-Lab-MDACC / CAPP_SEQ_pipeline

  ctdnaduplex-sequencingsingle-stranded-dna-sequencing
  Language:Shell 0

• dnbaker / BMFtools

  Barcoded Molecular Families

  ctdna
  Language:C++

• drvenki / sv-cfdna

  Structural Variants in cell-free tumor DNA

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

• MichaelEBryan / ctDNALiquidBiopsy

  Diagnostic performance of HPV-DeepSeek, a hybrid capture whole genome sequencing liquid biopsy for HPV-associated cancers

  classifiersctdnaneural-networksngs-analysis

• msk-access / bam_collapsing

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

  bam-collapsingworkflowmsk-accessduplexcwl-workflowctdnafgbio
  Language:Common Workflow Language

• msk-access / uncollapsed_bam_generation

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

  workflowcwl-workflowcwlumicfdnactdna
  Language:Common Workflow Language