Repositories list

• getzlab.github.io

  Public
  Getz Lab site

  HTML

  •55•4•0•0•Updated Nov 6, 2024Nov 6, 2024

• rnaseqc

  Public
  Fast, efficient RNA-Seq metrics for quality control and process optimization

  bioinformaticsrna-seqrnaseq

  C++

  •

  Other

  •19•149•18•1•Updated Nov 2, 2024Nov 2, 2024

• slurm_gcp_docker

  Public
  Spin up autoscaling Dockerized Slurm clusters on GCP

  Python

  •2•0•2•3•Updated Oct 24, 2024Oct 24, 2024

• DLBCL-Classifier

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• DLBclass-tool

  Public
  Jupyter Notebook

  •0•1•0•0•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

• PurityReviewer

  Public
  Suite of purity reviewers and review components

  Python

  •0•2•0•0•Updated Oct 9, 2024Oct 9, 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 Oct 4, 2024Oct 4, 2024

• PhylogicNDT

  Public
  Fork for adding Python 3/hg38 support to PhylogicNDT

  HTML

  •

  Other

  •39•0•0•1•Updated Sep 30, 2024Sep 30, 2024

• 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 Sep 27, 2024Sep 27, 2024

• van_allen_comut

  Public
  Van Allen CoMut package

  Python

  •

  MIT License

  •27•0•0•0•Updated Aug 29, 2024Aug 29, 2024

• SignatureAnalyzer

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

  Python

  •

  MIT License

  •21•72•3•0•Updated Aug 27, 2024Aug 27, 2024

• ABSOLUTE

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

  R

  •

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

  •5•7•2•0•Updated Aug 22, 2024Aug 22, 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

• dalmatian

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

  Python

  •13•18•8•0•Updated Jun 16, 2024Jun 16, 2024

• canine-tinkering

  Public
  Repo for tinkering with canine and submitting PRs

  Python

  •

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

  •6•0•0•0•Updated Apr 24, 2024Apr 24, 2024

• wolF_Mutect2

  Public
  somatic variation calling pipeline with GATK Mutect2 in wolF

  Python

  •1•0•1•1•Updated Apr 3, 2024Apr 3, 2024

• igv_remote

  Public
  A Python interface for interacting with IGV desktop over a port using IGV batch commands

  Python

  •3•5•1•0•Updated Mar 20, 2024Mar 20, 2024

• CApy

  Public
  Cancer Analysis tools in Python

  Python

  •3•3•1•0•Updated Mar 19, 2024Mar 19, 2024

• BTK_Growth_Kinetics_analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 22, 2024Feb 22, 2024

• CLUMPS

  Public
  Python

  •1•3•1•0•Updated Feb 16, 2024Feb 16, 2024

• CLUMPS-PTM

  Public
  CLUMPS adapted to post-translational modifications.

  Python

  •

  MIT License

  •0•8•1•0•Updated Jan 3, 2024Jan 3, 2024