Repositories list

• mushroom

  Public
  A computational tool for identification of 3D multi-modal spatial neighborhoods

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Nov 5, 2024Nov 5, 2024

• CromwellRunner

  Public
  Scripts for managing Cromwell workflows

  Shell

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 4, 2024Nov 4, 2024

• druggability_databases

  Public
  Python

  •0•1•0•0•Updated Oct 31, 2024Oct 31, 2024

• importGDC

  Public
  Automated download of CPTAC3 data from GDC

  Shell

  •0•2•0•0•Updated Oct 31, 2024Oct 31, 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 Oct 25, 2024Oct 25, 2024

• rcwrapper

  Public
  calculate vaf for variants based on bam

  Perl

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• somaticwrapper

  Public
  Detect somatic variants from tumor and normal WGS/WXS data

  Perl

  •

  GNU Affero General Public License v3.0

  •6•15•0•0•Updated Oct 2, 2024Oct 2, 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

• ST_subclone_publication

  Public
  Code for spatial subclone paper

  R

  •1•2•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

• 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

• 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•2•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

• 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