Repositories list

• HapASeg

  Public
  Priebe et al. 2026, Genome Biology

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•66 pull requests•Updated Jun 11, 2026Jun 11, 2026

• gbm_icb_manuscript

  Public
  Code for reproducing the figures in the Ghannam et al. GBM ICB manuscript

  Jupyter Notebook

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• CDK46_barcoding_paper

  Public
  Code for the CDK46 barcoding project with Rinath Jeselsohn

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• covcollect

  Public
  C++

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 21, 2026May 21, 2026

• walker

  Public
  C++ functions for walking HTS data

  C++

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 21, 2026May 21, 2026

• PhylogicNDT

  Public
  Fork for adding Python 3/hg38 support to PhylogicNDT

  HTML

  •

  Other

  •4646 forks•33 stars•00 issues•11 pull request•Updated May 21, 2026May 21, 2026

• het_pulldown_from_callstats_TOOL

  Public
  Call normal het sites and get their tumor coverage from a MuTect callstats file

  toolcnv

  toolcnv

  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated May 14, 2026May 14, 2026

• adipo_finder

  Public
  modules to identify adipocytes from segmentation masks, tested on IMC data

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• getzlab.github.io

  Public
  Getz Lab site

  HTML

  •6868 forks•44 stars•00 issues•22 pull requests•Updated Apr 13, 2026Apr 13, 2026

• canine

  Public
  A modular, high-performance computing solution to run jobs using Slurm

  bioinformaticsslurmhigh-performance-computing

  bioinformaticsslurmhigh-performance-computing

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •66 forks•88 stars•1313 issues•44 pull requests•Updated Apr 8, 2026Apr 8, 2026

• dalmatian

  Public
  dalmatian is a collection of high-level companion functions for Firecloud and FISS.

  Python

  •1313 forks•2020 stars•99 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• HapASeg_manuscript

  Public
  Code to reproduce the figures and results from Priebe et al. 2026

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 30, 2026Mar 30, 2026

• Rapid_Autopsy_Convergent_Evolution

  Public
  This repository contains code necessary to reproduce the results in the Rapid Autopsy Convergent Evolution paper

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• cnv_suite

  Public
  Compare, Visualize, and Simulate Copy Number Profiles

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •44 forks•22 stars•00 issues•22 pull requests•Updated Feb 24, 2026Feb 24, 2026

• BTC_epigenetics

  Public
  epigenetics of BTC atlas

  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 19, 2026Feb 19, 2026

• DLBCL-Classifier

  Public
  Jupyter Notebook

  •33 forks•77 stars•33 issues•11 pull request•Updated Feb 17, 2026Feb 17, 2026

• CLL_MRD_growth_kinetics

  Public
  Collection of notebooks in growth kinetics analysis for CLL MRD

  Jupyter Notebook

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 26, 2026Jan 26, 2026

• SignatureAnalyzer

  Public
  Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

  Python

  •

  MIT License

  •2222 forks•8484 stars•33 issues•00 pull requests•Updated Jan 20, 2026Jan 20, 2026

• ABSOLUTE

  Public
  ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •99 forks•1616 stars•22 issues•11 pull request•Updated Nov 5, 2025Nov 5, 2025

• slurm_gcp_docker

  Public
  Spin up autoscaling Dockerized Slurm clusters on GCP

  Python

  •22 forks•11 star•22 issues•33 pull requests•Updated Sep 7, 2025Sep 7, 2025

• rapidautopsyportal

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 3, 2025Sep 3, 2025

• MutSig2CV_refactored

  Public
  MutSig2CV from Lawrence et al. 2014

  MATLAB

  •

  Other

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Aug 12, 2025Aug 12, 2025

• BTK_Growth_Kinetics_analysis

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 8, 2025Aug 8, 2025

• Chaudhary_Moorhead_Head-Neck_ClinCanRes_Manuscript_2025

  Public
  Figures for Chaudhary, Moorhead et al 2025

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 8, 2025Aug 8, 2025

• Numbat-multiome_Analysis

  Public
  The repo containing the code/data/misc to reproduce figures contained in the manuscript of numbat-multiome

  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 21, 2025Jul 21, 2025

• neoag-tools

  Public
  Phasing and translation modules for neoantigen analysis

  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jul 16, 2025Jul 16, 2025

• KeiraSummerCode

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•11 pull request•Updated Jul 16, 2025Jul 16, 2025

• igv_gdc_buddy

  Public
  stream & update gdc signed url to IGV

  Python

  •00 forks•22 stars•22 issues•00 pull requests•Updated Jun 26, 2025Jun 26, 2025

• CloneSig

  Public
  Repository containing code for running CloneSig for identification of genes with convergent mutations

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 10, 2025Jun 10, 2025

• parsons_her2_tki_manuscript

  Public
  Code accompanying the Parsons HER2-amplified breast cancer/TKI manuscript

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 6, 2025Jun 6, 2025