cclab-brca

neoadjuvant-therapy-response-predictor

NGTAS_pipeline

Computational pipeline to analyse Next Generation Targeted Amplicon Sequence data

mutationalProfiles

brcarepred

Patterns-Immune-Infiltration

Contains data and annotation used in "Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study" (Ali HR et al. PLoS Med 2016)

ICRG

Example code to generate the In-silico Combined human-mouse Reference Genome (ICRG) to distinguish human and mouse reads in high-throughput sequencing experiments

MET-breast-landscapes

BCMC

clone-dynamics

Dynamics_TNBC_clinical_trial

BioRxiv https://doi.org/10.1101/2023.01.10.523259

HCI011_RNAseq

RNA-seq processed data and analysis code for the paper: FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (Ros et al 2020).

METABRIC_methylation_profiles

Contains data files used in "DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation" (Batra, Lifshitz et al. 2021).

scRNAseq_pipeline

Pipeline for processing scRNA-seq (10X) and Visium data