McGranahanLab

bioinfcollab_cruklungcentre

Bioinformatics collaboration at CRUK Lung center of excellence

CONIPHER

Git repo for CONIPHER tree building

CONIPHER-wrapper

Guidebook

HDP_sigExtraction

Pipeline to extract de novo mutational signatures using HDP.

LCCE_workshop_2023

mhc-hammer

Pipeline to detect HLA disruption from WES and RNAseq data

RVdriver

A statistical approach to detect cancer driver genes utilising the RNA Variant Allele Frequency of somatic mutations

T-cell-ExTRECT-figure-code-2021

Code used to produce figures in the paper "T cell quantification from DNA sequencing predicts immunotherapy response " by Bentham et al 2021

TcellExTRECT

McGranahanLab/TcellExTRECT

McGranahanLab/CONIPHER

Git repo for CONIPHER tree building

McGranahanLab/mhc-hammer

Pipeline to detect HLA disruption from WES and RNAseq data

McGranahanLab/CONIPHER-wrapper

McGranahanLab/T-cell-ExTRECT-figure-code-2021

Code used to produce figures in the paper "T cell quantification from DNA sequencing predicts immunotherapy response " by Bentham et al 2021

McGranahanLab/Guidebook

McGranahanLab/HDP_sigExtraction

Pipeline to extract de novo mutational signatures using HDP.

McGranahanLab/bioinfcollab_cruklungcentre

Bioinformatics collaboration at CRUK Lung center of excellence

McGranahanLab/RVdriver

A statistical approach to detect cancer driver genes utilising the RNA Variant Allele Frequency of somatic mutations

McGranahanLab/LCCE_workshop_2023

McGranahanLab/ACTdiscover

Method to detect aneuploidy in circulating tumor DNA

McGranahanLab/ALPACA-paper

McGranahanLab/MCL1amplification

Code used for analysis of the paper "MCL-1 gains occur with high frequency in lung adenocarcinoma and can be targeted therapeutically" by Munkhbaatar et al.

McGranahanLab/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

McGranahanLab/ARTanalysis

Code to recreate the Figure of the manuscript “Replication timing alterations shape the genomic and transcriptomic landscape during breast and lung cancer evolution”

McGranahanLab/GEL_lung_landscape_figure_code

Figure code for the GEL lung landscape paper

McGranahanLab/mutect2_forceActive_behaviour

McGranahanLab/ACTdiscover-figure-code-2023

McGranahanLab/Noncoding_drivers_Nextflow

Nextflow pipeline for the de-novo detection of coding and noncoding cancer driver genomic elements in cohorts of cancer patients.

McGranahanLab/RepliSeqPipeline

Pipeline to process fastq files provided by the Repli-Seq protocol of G1, early S-phase and late S-phase reads

McGranahanLab/TX_data