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    134 repositories

    • somaticwrapper

      Public
      Detect somatic variants from tumor and normal WGS/WXS data
      Perl
      •
      GNU Affero General Public License v3.0
      •5•15•0•0•Updated Oct 2, 2024Oct 2, 2024

    • mushroom

      Public
      A computational tool for identification of 3D multi-modal spatial neighborhoods
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • SomaticSV

      Public
      CWL wrapper for Manta 1.4.0 and simple filter
      Shell
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Aug 30, 2024Aug 30, 2024

    • CromwellRunner

      Public
      Scripts for managing Cromwell workflows
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 30, 2024Aug 30, 2024

    • ST_subclone_publication

      Public
      Code for spatial subclone paper
      R
      •1•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • PanCan_snATAC_publication

      Public
      Jupyter Notebook
      •4•13•2•0•Updated Aug 4, 2024Aug 4, 2024

    • druggability

      Public
      Python
      •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

    • CPTAC_PanCan_Signature_analysis

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • importGDC

      Public
      Automated download of CPTAC3 data from GDC
      Shell
      •0•2•0•0•Updated May 16, 2024May 16, 2024

    • Intratumor_heterogeneity

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated May 15, 2024May 15, 2024

    • Immune_snATAC

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated May 15, 2024May 15, 2024

    • mnp_filter

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated May 15, 2024May 15, 2024

    • ASE_analysis

      Public
      R
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • GDC.case.discover

      Public
      Obtain submitted reads and clinical info associated with CPTAC3 cases
      Shell
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Apr 24, 2024Apr 24, 2024

    • LR_SV_pipe

      Public
      Call SVs from long-read sequencing data
      Perl
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • morph

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • WUDocker

      Public
      Utilities for launching docker in various Washington University environments
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • Fusion_hg38

      Public
      Shell
      •0•1•6•0•Updated Feb 19, 2024Feb 19, 2024

    • germlinewrapper

      Public
      detect germline variants from normal samples
      Perl
      •
      GNU General Public License v3.0
      •3•4•0•0•Updated Feb 12, 2024Feb 12, 2024

    • monopogen_pipeline

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • clinvar

      Public
      This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
      Python
      •
      Other
      •55•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • HTAN_BRCA_publication

      Public
      R
      •2•1•0•0•Updated Jan 10, 2024Jan 10, 2024

    • druggability_databases

      Public
      Python
      •0•1•0•0•Updated Dec 6, 2023Dec 6, 2023

    • ancestry-pipeline

      Public
      Ding lab ancestry pipeline
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • ccRCC_snRNA_analysis

      Public
      R
      •5•6•0•0•Updated Oct 4, 2023Oct 4, 2023

    • ffpefiltering

      Public
      Use MicroSec for FFPE filtering
      R
      •0•0•0•0•Updated Sep 7, 2023Sep 7, 2023

    • pecgs-pipeline

      Public
      Common Workflow Language
      •1•0•1•0•Updated Aug 25, 2023Aug 25, 2023

    • TinJasmine

      Public
      CWL germline variant caller
      Common Workflow Language
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Aug 24, 2023Aug 24, 2023

    • Pindel_GermlineCaller

      Public
      CWL project with Pindel germline calling and filtering
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 24, 2023Aug 24, 2023

    • SomaticHaplotype

      Public
      Object-oriented tools for phase block analysis and somatic mutation phasing using linked-read WGS
      R
      •
      MIT License
      •0•1•0•0•Updated Aug 14, 2023Aug 14, 2023