Repositories list

• FSAudit

  Public
  Filesystem audit visualization

  Shell

  •0•1•0•0•Updated Feb 23, 2026Feb 23, 2026

• SRescue

  Public
  Pipeline for SR-LR integration

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• SVLover

  Public
  LOng read Variant ExploreR

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• VirusScan

  Public
  VirusScan Pipeline

  Perl

  •7•12•0•0•Updated Feb 7, 2026Feb 7, 2026

• mCRC_publication

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• ffpefiltering

  Public
  Use MicroSec for FFPE filtering

  R

  •1•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• rcwrapper

  Public
  calculate vaf for variants based on bam

  Perl

  •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

• somaticwrapper

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

  Perl

  •

  GNU Affero General Public License v3.0

  •9•19•1•0•Updated Jan 29, 2026Jan 29, 2026

• Long_read_RCC

  Public
  0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• IRD

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

• morph

  Public
  Python

  •

  MIT License

  •3•14•1•0•Updated Oct 24, 2025Oct 24, 2025

• ONTsplice

  Public
  pipeline for processing ONT RNA-Seq data

  Perl

  •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

• ding-lab-spatial

  Public
  misc. spatial analyses for the Ding lab.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 30, 2025Sep 30, 2025

• importGDC

  Public
  Automated download of CPTAC3 data from GDC

  Shell

  •0•2•0•0•Updated Sep 16, 2025Sep 16, 2025

• 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 Sep 4, 2025Sep 4, 2025

• mushroom

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

  Jupyter Notebook

  •

  MIT License

  •1•15•2•0•Updated Aug 1, 2025Aug 1, 2025

• SenNet_liver

  Public
  HTML

  •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• normal_mouse_kidney_scripts

  Public
  R

  •1•6•2•0•Updated May 8, 2025May 8, 2025

• LR_SV_pipe

  Public
  Call SVs from long-read sequencing data

  Python

  •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

• spatial_driver_co-detection_paper

  Public
  Code for spatial driver co-detection paper

  R

  •1•1•0•0•Updated Mar 19, 2025Mar 19, 2025

• ST_subclone_publication

  Public
  Code for spatial subclone paper

  R

  •4•16•4•0•Updated Jan 23, 2025Jan 23, 2025

• co-evolution_myeloma_-2021

  Public
  0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• pecgs-pipeline

  Public
  Common Workflow Language

  •2•1•1•0•Updated Nov 21, 2024Nov 21, 2024

• druggability_databases

  Public
  Python

  •0•1•0•0•Updated Nov 10, 2024Nov 10, 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

• 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

• PanCan_snATAC_publication

  Public
  Jupyter Notebook

  •5•20•4•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