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ambra1_paper

Scripts to reproduce results of "The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability" Chaikovsky et al. Nature 2021

amplification_outliers

Code to reproduce the paper "Funtional screenings of amplification outlier oncogenes in organoid models of early tumorigenesis"

breastcancerith

breastcancerspatialproteomics

chromatinanthra

Source code from the manuscript "Chromatin Regulators Mediate Anthracycline Sensitivity in Breast Cancer"

cookiecutter-reproducible-science

boilerplate for reproducible and transparent science

gastric_organoid_evolution

Deterministic evolution and stringent selection during pre-neoplasia

germline-epitopes

Scripts for evaluating germline-derived epitopes (Houlahan et al., 2023)

htan-dcis

Scripts to recapitulate analysis of HTAN DCIS Atlas

mcrcs

A computational framework for multi-region exome data analysis

microwell_ngs

pan-metastasis

scimet

Spatial Computational Inference of MEtastatic Timing (SCIMET)

triob07

These are the processed data files related to the bulk expression data from breast tumors treated on the TRIO B07 trial (NCT00769470). Tumor or tumor bed tissue was collected and subjected to the Agilent Whole Human Genome 44K 2-color chip pre-treatment, on-treatment (after 1 cycle of HER2-targeted therapy alone, either trastuzumab, lapatinib, or the combination), and post-treatment (at definitive surgery after 6 cycles of docetaxel/carboplatin in combination with assigned HER2-targeted therapy). The raw data is available at GEO (GSE130788). The folder also includes the full protocol for the TRIO B07 trial and the gene sets assessed.

vap

Variant Assurance Pipeline

virtualtumorevolution

Spatial Simulation of Tumor Growth