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    82 repositories

    • SNVReviewer

      Public
      AnnoMate Reviewer for annotating and comparing single nucleotide variant(SNV)
      Python
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • getzlab.github.io

      Public
      Getz Lab site
      HTML
      •60•4•0•1•Updated Mar 10, 2025Mar 10, 2025

    • SVelfie

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • neoag-tools

      Public
      Phasing and translation modules for neoantigen analysis
      Python
      •2•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • PurityReviewer

      Public
      Suite of purity reviewers and review components
      Jupyter Notebook
      •0•2•0•1•Updated Mar 5, 2025Mar 5, 2025

    • SVelfie_old_production_repo_delete

      Public
      SVelfie (equivalent to v14 of the previously named SSVGAR module"
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 3, 2025Mar 3, 2025

    • DIGDriver

      Public
      Lab-internal version of DIG
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • canine

      Public
      A modular, high-performance computing solution to run jobs using SLURM
      bioinformaticshigh-performance-computingslurm
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•6•14•3•Updated Feb 28, 2025Feb 28, 2025

    • AsymTools2

      Public
      AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.
      MATLAB
      •
      Other
      •1•2•0•0•Updated Feb 25, 2025Feb 25, 2025

    • SignatureAnalyzer

      Public
      Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
      Python
      •
      MIT License
      •21•77•3•0•Updated Feb 21, 2025Feb 21, 2025

    • DLBCL-Classifier

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Feb 3, 2025Feb 3, 2025

    • dalmatian

      Public
      dalmatian is a collection of high-level companion functions for Firecloud and FISS.
      Python
      •13•18•8•0•Updated Jan 27, 2025Jan 27, 2025

    • BRCA_ctDNA_Landscape

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • ABSOLUTE

      Public
      ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •6•7•2•0•Updated Jan 16, 2025Jan 16, 2025

    • slurm_gcp_docker

      Public
      Spin up autoscaling Dockerized Slurm clusters on GCP
      Python
      •2•0•2•3•Updated Nov 20, 2024Nov 20, 2024

    • cnv_suite

      Public
      Compare, Visualize, and Simulate Copy Number Profiles
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•2•0•2•Updated Nov 12, 2024Nov 12, 2024

    • rnaseqc

      Public
      Fast, efficient RNA-Seq metrics for quality control and process optimization
      bioinformaticsrna-seqrnaseq
      C++
      •
      Other
      •19•158•18•1•Updated Nov 2, 2024Nov 2, 2024

    • DLBclass-tool

      Public
      Jupyter Notebook
      •1•2•1•1•Updated Oct 23, 2024Oct 23, 2024

    • dig_test_mutation_burden

      Public
      This repo contains scripts that, given a mutation map, test coding and non-coding regions for positive selection and generate html reports.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • gbm_icb_manuscript

      Public
      Code for reproducing the figures in the Ghannam et al. GBM ICB manuscript
      Jupyter Notebook
      •0•1•0•0•Updated Oct 17, 2024Oct 17, 2024

    • PhylogicNDT

      Public
      Fork for adding Python 3/hg38 support to PhylogicNDT
      HTML
      •
      Other
      •41•3•0•1•Updated Sep 30, 2024Sep 30, 2024

    • van_allen_comut

      Public
      Van Allen CoMut package
      Python
      •
      MIT License
      •27•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • parsons_her2_tki_manuscript

      Public
      Code accompanying the Parsons HER2-amplified breast cancer/TKI manuscript
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • walker

      Public
      C++ functions for walking HTS data
      C++
      •1•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • AnnoMate

      Public
      Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets
      Python
      •
      MIT License
      •1•7•1•0•Updated Aug 5, 2024Aug 5, 2024

    • AnnoMateTemplate

      Public
      Template Repo for generating new JupyterReviewer Suites
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • PhylogicNDTReviewer

      Public
      Interactive app to review Phylogic solutions and data.
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jul 31, 2024Jul 31, 2024

    • CancerPatientReviewer

      Public
      Explore integrated data on the patient level interactively in a Dash App, powered by JupyterReviewer
      Jupyter Notebook
      •1•0•1•0•Updated Jul 31, 2024Jul 31, 2024

    • MutationReviewer

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • SimulatedTumorData

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024