getzlab

Pinned Repositories

10x-cd45-isoform-quantification
Language:Jupyter Notebook70
Boiarsky-etal-2022
Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022
Language:Jupyter Notebook6 8 02
CPTAC_PanCan_PTM_2023
Language:Jupyter Notebook131
dalmatian
dalmatian is a collection of high-level companion functions for Firecloud and FISS.
Language:Python18 17 2312
deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Language:Jupyter Notebook48 6 2321
Haradhvala_et_al_2022
Language:Jupyter Notebook80
MutSig2CV
MutSig2CV from Lawrence et al. 2014
Language:MATLAB28 6 306
rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
Language:C++141 11 7119
scrinvex
Single Cell RNA Intron-Exon counting
Language:C++11 9 24
SignatureAnalyzer
Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
Language:Python67 10 3720

getzlab's Repositories

getzlab/rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
Language:C++141 11 7119
getzlab/SignatureAnalyzer
Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
Language:Python67 10 3720
getzlab/dalmatian
dalmatian is a collection of high-level companion functions for Firecloud and FISS.
Language:Python18 17 2312
getzlab/CPTAC_PanCan_PTM_2023
Language:Jupyter Notebook131
getzlab/Haradhvala_et_al_2022
Language:Jupyter Notebook80
getzlab/ABSOLUTE
ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38
Language:R65
getzlab/Boiarsky-etal-2022
Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022
Language:Jupyter Notebook6 8 02
getzlab/canine
A modular, high-performance computing solution to run jobs using SLURM
Language:Python6 10 396
getzlab/CLUMPS-PTM
CLUMPS adapted to post-translational modifications.
Language:Python6 6 10
getzlab/AnnoMate
Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets
Language:Python51
getzlab/igv_remote
A Python interface for interacting with IGV desktop over a port using IGV batch commands
Language:Python5 3 23
getzlab/getzlab.github.io
Getz Lab site
Language:HTML4 2 01
getzlab/CApy
Cancer Analysis tools in Python
Language:Python3 6 13
getzlab/CLUMPS
Language:Python3 18 11
getzlab/CLUMPS2
Re-factored code for CLUMPS.
Language:Python2 13 2
getzlab/cnv_suite
Compare, Visualize, and Simulate Copy Number Profiles
Language:Jupyter Notebook2 2 03
getzlab/PurityReviewer
Suite of purity reviewers and review components
Language:Jupyter Notebook2 8 0
getzlab/AsymTools2
AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.
Language:MATLAB1 6 0
getzlab/slurm_gcp_docker
Spin up autoscaling Dockerized Slurm clusters on GCP
Language:Python0 4 102
getzlab/ASCAT-parser
Parsing tool from ASCATNGS to alleliccapseg output to use with ABSOLUTE
Language:Python7 0
getzlab/BTK_Growth_Kinetics_analysis
Language:Jupyter Notebook8 0
getzlab/CancerPatientReviewer
Explore integrated data on the patient level interactively in a Dash App, powered by JupyterReviewer
Language:Jupyter Notebook1
getzlab/canine-tinkering
Repo for tinkering with canine and submitting PRs
Language:Python1 0
getzlab/MutationReviewer
Language:Python8 0
getzlab/mutect
MuTect -- Accurate and sensitive cancer mutation detection
Language:Java
getzlab/parsons_her2_tki_manuscript
Code accompanying the Parsons HER2-amplified breast cancer/TKI manuscript
Language:HTML8 0
getzlab/PhylogicNDT
Fork for adding Python 3/hg38 support to PhylogicNDT
Language:HTML1 02
getzlab/PhylogicNDTReviewer
Interactive app to review Phylogic solutions and data.
Language:Jupyter Notebook1
getzlab/SimulatedTumorData
Language:Jupyter Notebook
getzlab/wolF_Mutect2
somatic variation calling pipeline with GATK Mutect2 in wolF
Language:Python1