Repositories list

• Mutation_Clonality

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

  R

  •0•1•0•0•Updated Sep 25, 2024Sep 25, 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

• tumor-only-snakemake

  Public
  Python

  •0•0•0•0•Updated Jul 18, 2024Jul 18, 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 Jun 24, 2024Jun 24, 2024

• BLADE

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

  HTML

  •

  MIT License

  •4•25•1•1•Updated Apr 3, 2024Apr 3, 2024

• QDNAseq.snakemake

  Public
  JavaScript

  •1•1•0•0•Updated Mar 12, 2024Mar 12, 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

• 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 Nov 24, 2020Nov 24, 2020

• 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