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@cancersysbio Curtis Lab. Stanford School of Medicine

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    23 repositories

    • ai-ml-jc

      Public
      AI/ML Journal Club
      Jupyter Notebook
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • AmpliconSuite-pipeline

      Public
      A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes Amp…
      Python
      •
      Other
      •32•0•0•1•Updated Apr 9, 2026Apr 9, 2026

    • BERGERON

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Jan 31, 2026Jan 31, 2026

    • CRAWFORD

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Jan 31, 2026Jan 31, 2026

    • ecDNAInspector

      Public
      ecDNAInspector (ecI) provides a systematic method for ecDNA structural validation and analysis, enabling higher-confidence utilization of sequencing data-based …
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • HTAN-FAP

      Public
      Code base for HTAN-FAP PreCancer Atlas - doi: 10.1101/2025.09.08.674484
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • breast-architecture

      Public
      R
      •
      MIT License
      •0•5•1•0•Updated Jan 2, 2025Jan 2, 2025

    • germline-epitopes

      Public
      Scripts for evaluating germline-derived epitopes (Houlahan et al., 2023)
      R
      •
      MIT License
      •0•1•0•0•Updated Sep 5, 2024Sep 5, 2024

    • VAP

      Public
      Variant Assurance Pipeline
      Perl
      •3•5•1•0•Updated Oct 13, 2023Oct 13, 2023

    • amplification_outliers

      Public
      Code to reproduce the paper "Funtional screenings of amplification outlier oncogenes in organoid models of early tumorigenesis"
      R
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • microwell_NGS

      Public
      0•0•0•0•Updated Aug 1, 2023Aug 1, 2023

    • htan-DCIS

      Public
      Scripts to recapitulate analysis of HTAN DCIS Atlas
      R
      •0•1•0•0•Updated Jun 9, 2023Jun 9, 2023

    • gastric_organoid_evolution

      Public
      Deterministic evolution and stringent selection during pre-neoplasia
      genomicscancer-genomicstumor-evolution
      genomicscancer-genomicstumor-evolutionorganoidsgastric
      HTML
      •1•7•0•0•Updated Jun 3, 2023Jun 3, 2023

    • cookiecutter-reproducible-science

      Public
      boilerplate for reproducible and transparent science
      Other
      •94•0•0•0•Updated Oct 25, 2022Oct 25, 2022

    • chromatinAnthra

      Public
      Source code from the manuscript "Chromatin Regulators Mediate Anthracycline Sensitivity in Breast Cancer"
      R
      •3•5•0•0•Updated Mar 15, 2022Mar 15, 2022

    • BreastCancerSpatialProteomics

      Public
      Jupyter Notebook
      •5•3•0•0•Updated Feb 14, 2021Feb 14, 2021

    • AMBRA1_paper

      Public
      Scripts to reproduce results of "The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability" Chaikovsky et al. Nature 2021
      R
      •0•0•0•0•Updated Jan 26, 2021Jan 26, 2021

    • TRIOB07

      Public
      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…
      0•0•0•0•Updated Oct 29, 2020Oct 29, 2020

    • pan-metastasis

      Public
      Python
      •5•9•0•0•Updated May 16, 2020May 16, 2020

    • mCRCs

      Public
      A computational framework for multi-region exome data analysis
      R
      •8•9•1•0•Updated Apr 9, 2020Apr 9, 2020

    • SCIMET

      Public
      Spatial Computational Inference of MEtastatic Timing (SCIMET)
      Python
      •12•14•0•0•Updated May 28, 2019May 28, 2019

    • BreastCancerITH

      Public
      treatment-effectsbreast-cancerheterogeneity
      treatment-effectsbreast-cancerheterogeneitycancer-evolution
      Python
      •2•2•0•0•Updated Aug 17, 2018Aug 17, 2018

    • VirtualTumorEvolution

      Public
      Spatial Simulation of Tumor Growth
      Python
      •11•14•2•0•Updated Feb 24, 2017Feb 24, 2017
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