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    38 repositories

    • tempe

      Public
      A container focused and streamlined iteration of the Phoenix pipeline
      Jinja
      •
      GNU General Public License v3.0
      •1•2•15•0•Updated Nov 20, 2024Nov 20, 2024

    • containers

      Public
      Dockerfile
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • snpSniffer

      Public
      Tool for checking genotype concordance between multiple assays
      Java
      •
      MIT License
      •3•0•1•0•Updated Aug 10, 2024Aug 10, 2024

    • phoenix

      Public
      Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
      EJS
      •
      MIT License
      •6•17•42•1•Updated May 20, 2024May 20, 2024

    • jetstream_resources

      Public
      Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
      Shell
      •
      MIT License
      •1•3•4•0•Updated Feb 21, 2024Feb 21, 2024

    • banovichlab

      Public
      Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).
      R
      •
      MIT License
      •14•42•0•0•Updated Feb 9, 2024Feb 9, 2024

    • jetstream

      Public
      Workflow management system written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers
      Python
      •
      MIT License
      •3•16•18•1•Updated Jan 11, 2024Jan 11, 2024

    • vcfMerger2

      Public
      Dynamic vcfMerger for 2 to N somatic variants vcf files
      vcfsvariant-callerssomatic-vcfs
      Python
      •
      Other
      •1•5•1•0•Updated Sep 11, 2023Sep 11, 2023

    • Keats_Lab_Public

      Public
      Public resources from the Keats Lab at TGen
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • MMRF_CoMMpass

      Public
      A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.
      Shell
      •
      MIT License
      •7•18•4•0•Updated Apr 17, 2023Apr 17, 2023

    • jetstream_containers

      Public
      Containers for running TGen Jetstream pipelines
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

    • manta

      Public
      Structural variant and indel caller for mapped sequencing data
      C++
      •
      GNU General Public License v3.0
      •154•0•0•0•Updated Nov 8, 2022Nov 8, 2022

    • gencode-plus-lncipedia

      Public
      non-redundant genome annotation combining GENCODE 29 and lncipedia 5.2
      R
      •0•0•0•0•Updated Aug 19, 2022Aug 19, 2022

    • tgen-jetstream-docs

      Public
      0•0•0•0•Updated Nov 4, 2021Nov 4, 2021

    • Post_Medusa_Processing

      Public
      Shell
      •
      MIT License
      •0•1•0•0•Updated Sep 27, 2021Sep 27, 2021

    • coyote

      Public
      EJS
      •
      MIT License
      •0•1•1•0•Updated Sep 19, 2021Sep 19, 2021

    • CovGen

      Public
      Creates a target specific exome_full192.coverage.txt file required by MutSig
      Python
      •
      MIT License
      •9•21•2•1•Updated Sep 15, 2021Sep 15, 2021

    • MARS

      Public
      Check the purity of a multiple myeloma tumor sample with this tool.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 3, 2021Aug 3, 2021

    • docker_factory

      Public
      Create docker images from scratch
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jul 14, 2021Jul 14, 2021

    • ichorCNA

      Public
      Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
      R
      •
      GNU General Public License v3.0
      •89•0•0•0•Updated Apr 27, 2021Apr 27, 2021

    • bisbee

      Public
      alternative splicing analysis pipeline
      Python
      •
      MIT License
      •4•17•10•1•Updated Apr 9, 2021Apr 9, 2021

    • GemDb38

      Public
      Perl
      •0•0•0•0•Updated Feb 24, 2021Feb 24, 2021

    • ppmi-rnaseq-wb-paper

      Public
      code used to generate figures for the ppmi whole blood rnaseq paper
      R
      •1•2•0•0•Updated Dec 18, 2020Dec 18, 2020

    • lumosVar2

      Public
      Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
      MATLAB
      •
      MIT License
      •1•10•4•0•Updated Oct 29, 2020Oct 29, 2020

    • gvm

      Public
      Replacement for LumosVar preprocess step
      C
      •
      MIT License
      •0•2•2•0•Updated Oct 8, 2020Oct 8, 2020

    • ppmi-qc-wt-paper

      Public
      QC of whole blood whole transcriptome for PPMI
      R
      •2•3•1•0•Updated Oct 2, 2020Oct 2, 2020

    • GemDb

      Public
      GemDb mongo variants/annotations hub
      mongoannotationsvariantsdrug-rulesbuild38build37
      Python
      •1•1•3•0•Updated Oct 2, 2020Oct 2, 2020

    • pegasusPipe

      Public
      Shell
      •
      MIT License
      •0•1•14•0•Updated Sep 25, 2020Sep 25, 2020

    • Institutional_Instructions

      Public
      Description of institutional rules and regulations regarding the usage of github, plus usage guidelines
      Shell
      •1•3•0•0•Updated Sep 21, 2020Sep 21, 2020

    • GemDb37

      Public
      Variant database for human genome build 37, includes public annotations and various TGen projects.
      Perl
      •0•0•0•0•Updated Jul 7, 2020Jul 7, 2020