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Tumor Genome Analysis Core

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  1. BLADE BLADE Public

    BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data

    HTML 26 4

  2. ACE ACE Public

    Absolute Copy Number Estimation using low-coverage whole genome sequencing data

    R 14 6

  3. OncoBLADE OncoBLADE Public

    Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution

    Jupyter Notebook 4

  4. WES-snake WES-snake Public

    snakemake from fastq to annotated mutation calling using MUTECT2

    R 2

  5. falco falco Public

    Amplicon variant caller

    R 1

  6. QDNAseq.dev QDNAseq.dev Public

    R 1

Repositories

Showing 10 of 23 repositories
  • Mutation_Clonality Public

    Clonality assesment in the TRACERx cohort using mutations detected by multiple panels

    tgac-vumc/Mutation_Clonality’s past year of commit activity
    R 1 0 0 0 Updated Nov 13, 2024
  • OncoBLADE Public

    Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution

    tgac-vumc/OncoBLADE’s past year of commit activity
    Jupyter Notebook 4 MIT 0 0 0 Updated Oct 24, 2024
  • translocation-snake Public

    Translocation detection pipeline by next generation sequencing. A combined approach of BreaKmer, Gridss, Wham and novoBreak.

    tgac-vumc/translocation-snake’s past year of commit activity
    JavaScript 0 0 0 0 Updated Oct 22, 2024
  • tumor-only-snakemake Public
    tgac-vumc/tumor-only-snakemake’s past year of commit activity
    Python 0 0 0 0 Updated Oct 22, 2024
  • QDNAseq.snakemake Public
    tgac-vumc/QDNAseq.snakemake’s past year of commit activity
    JavaScript 1 1 0 0 Updated Oct 22, 2024
  • CNA_clonality Public

    Code associated with manuscript "Diagnostic test accuracy to determine clonality between multiple tumors with pulmonary involvement using genome-wide copy number analysis"

    tgac-vumc/CNA_clonality’s past year of commit activity
    R 0 0 0 0 Updated Sep 25, 2024
  • CopywritR-snake Public

    Estimate copy number read counts from whole-exome sequencing data using CopyWritR

    tgac-vumc/CopywritR-snake’s past year of commit activity
    R 0 0 0 0 Updated Jul 31, 2024
  • BLADE Public

    BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data

    tgac-vumc/BLADE’s past year of commit activity
    HTML 26 MIT 4 1 1 Updated Apr 3, 2024
  • WES-snake Public

    snakemake from fastq to annotated mutation calling using MUTECT2

    tgac-vumc/WES-snake’s past year of commit activity
    R 2 0 0 0 Updated Jan 31, 2024
  • TCGA_purity Public
    tgac-vumc/TCGA_purity’s past year of commit activity
    R 1 0 0 0 Updated Nov 2, 2023
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