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@tgac-vumc Tumor Genome Analysis Core

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    24 repositories

    • OncoBLADEweb

      Public
      Website for BLADE
      JavaScript
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • Mutation_Clonality

      Public
      Clonality assesment in the TRACERx cohort using mutations detected by multiple panels
      R
      •0•1•0•0•Updated Nov 13, 2024Nov 13, 2024

    • OncoBLADE

      Public
      Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Oct 24, 2024Oct 24, 2024

    • translocation-snake

      Public
      Translocation detection pipeline by next generation sequencing. A combined approach of BreaKmer, Gridss, Wham and novoBreak.
      JavaScript
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • tumor-only-snakemake

      Public
      Python
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • QDNAseq.snakemake

      Public
      JavaScript
      •1•1•0•0•Updated Oct 22, 2024Oct 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"
      R
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • CopywritR-snake

      Public
      Estimate copy number read counts from whole-exome sequencing data using CopyWritR
      R
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • BLADE

      Public
      BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data
      HTML
      •
      MIT License
      •4•26•1•1•Updated Apr 3, 2024Apr 3, 2024

    • WES-snake

      Public
      snakemake from fastq to annotated mutation calling using MUTECT2
      R
      •0•2•0•0•Updated Jan 31, 2024Jan 31, 2024

    • TCGA_purity

      Public
      R
      •0•1•0•0•Updated Nov 2, 2023Nov 2, 2023

    • ACE

      Public
      Absolute Copy Number Estimation using low-coverage whole genome sequencing data
      R
      •6•14•3•1•Updated May 30, 2023May 30, 2023

    • spatstat_vectra

      Public
      Marked point process modeling of Vectra data
      HTML
      •1•0•0•0•Updated May 3, 2023May 3, 2023

    • lgg-snakemake

      Public
      Snakemake pipeline for analysis of methylation data of long and short survivors of 1p/19q-codeleted oligodendroglioma
      R
      •1•0•0•0•Updated Aug 30, 2021Aug 30, 2021

    • RNA-seq

      Public
      RNA-seq analysis pipeline based on Snakemake
      Python
      •5•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • small_scripts

      Public
      small things to be shared with others.
      R
      •0•0•0•0•Updated Jun 10, 2020Jun 10, 2020

    • CGHbase

      Public
      R
      •3•0•0•1•Updated Mar 8, 2019Mar 8, 2019

    • ddPCR

      Public
      R
      •0•1•0•1•Updated Dec 15, 2017Dec 15, 2017

    • QDNAseq.dev

      Public
      R
      •0•1•1•0•Updated Oct 6, 2017Oct 6, 2017

    • WECCA

      Public
      Weighted hierarchical clustering of array CGH data using (call probabilities)
      R
      •0•0•0•0•Updated Nov 30, 2015Nov 30, 2015

    • CGHcall

      Public
      R
      •1•0•3•0•Updated Nov 28, 2015Nov 28, 2015

    • QDNAseq.hg19

      Public
      R
      •3•0•1•0•Updated Sep 30, 2015Sep 30, 2015

    • QDNAseq.mm10

      Public
      R
      •0•0•0•0•Updated Sep 30, 2015Sep 30, 2015

    • falco

      Public
      Amplicon variant caller
      R
      •0•1•1•0•Updated Feb 23, 2015Feb 23, 2015