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getzlab

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rnaseqc

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

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SignatureAnalyzer

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

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dalmatian

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

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CPTAC_PanCan_PTM_2023

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Haradhvala_et_al_2022

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ABSOLUTE

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

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Boiarsky-etal-2022

Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022

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canine

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

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CLUMPS-PTM

CLUMPS adapted to post-translational modifications.

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AnnoMate

Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets

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igv_remote

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

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getzlab.github.io

Getz Lab site

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CApy

Cancer Analysis tools in Python

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CLUMPS

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CLUMPS2

Re-factored code for CLUMPS.

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cnv_suite

Compare, Visualize, and Simulate Copy Number Profiles

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PurityReviewer

Suite of purity reviewers and review components

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AsymTools2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.

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slurm_gcp_docker

Spin up autoscaling Dockerized Slurm clusters on GCP

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ASCAT-parser

Parsing tool from ASCATNGS to alleliccapseg output to use with ABSOLUTE

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BTK_Growth_Kinetics_analysis

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CancerPatientReviewer

Explore integrated data on the patient level interactively in a Dash App, powered by JupyterReviewer

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canine-tinkering

Repo for tinkering with canine and submitting PRs

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MutationReviewer

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mutect

MuTect -- Accurate and sensitive cancer mutation detection

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parsons_her2_tki_manuscript

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

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PhylogicNDT

Fork for adding Python 3/hg38 support to PhylogicNDT

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PhylogicNDTReviewer

Interactive app to review Phylogic solutions and data.

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SimulatedTumorData

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wolF_Mutect2

somatic variation calling pipeline with GATK Mutect2 in wolF

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