Li Ding's Lab

Repositories

• SeqQEst

  Do quality control for BAMs
  Python 0 0 0 0 Updated Feb 8, 2021

• TinDaisy

  CWL version of SomaticWrapper
  Common Workflow Language 1 3 0 0 Updated Feb 2, 2021

• CPTAC3.catalog

  Details about CPTAC3 data at GDC and in Ding Lab
  Shell 1 1 1 0 Updated Jan 27, 2021

• PDX-PanCanAtlas
  Jupyter Notebook 0 0 0 0 Updated Jan 23, 2021

• cptac_methylation

  Methylation array analysis pipeline for CPTAC
  R 3 3 0 0 Updated Jan 21, 2021

• exportGDC

  Utilities to copy GDC-controlled BamMap data across systems
  Shell 0 0 0 0 Updated Jan 21, 2021

• CPTAC3.case.discover

  Obtain submitted reads and clinical info associated with CPTAC3 cases
  Shell GPL-3.0 1 0 0 0 Updated Jan 20, 2021

• BICSEQ2

  BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA
  Shell GPL-3.0 1 2 1 0 Updated Jan 13, 2021

• importGDC.CPTAC3

  Automated download of CPTAC3 data from GDC
  Shell 0 1 0 0 Updated Jan 12, 2021

• msisensor Archived

  microsatellite instability detection using tumor only or paired tumor-normal data

  bam-files cancer-genomics msi msi-score
  C++ MIT 45 103 10 1 Updated Jan 6, 2021

• ccRCC_snRNA_analysis
  R 3 0 0 0 Updated Dec 18, 2020

• mutct
  R 0 0 0 0 Updated Dec 18, 2020

• pollock

  A tool that classifies cells based on their gene expression
  Jupyter Notebook BSD-3-Clause 1 0 0 1 Updated Dec 9, 2020

• CromwellRunner

  Scripts for managing Cromwell workflows
  Shell GPL-3.0 0 0 0 0 Updated Dec 2, 2020

• misplice

  Discover Mutation Induced Splice Sites
  Perl GPL-3.0 5 5 0 0 Updated Nov 29, 2020

• FSAudit

  Filesystem audit visualization
  Shell 0 0 0 0 Updated Nov 6, 2020

• SomaticHaplotype

  Object-oriented tools for phase set analysis and somatic mutation phasing using linked-read WGS
  R MIT 0 0 0 0 Updated Nov 3, 2020

• somaticwrapper

  Detect somatic variants from tumor and normal exome data
  Perl AGPL-3.0 2 6 0 0 Updated Oct 30, 2020

• VEP_Filter

  TinDaisy modules for filtering VCF based on VEP annotation
  Shell GPL-3.0 0 1 0 0 Updated Oct 17, 2020

• VLD_FilterVCF

  CWL implementation of VCF filter for variant VAF, length, read depth, and allelic depth
  Python GPL-3.0 0 0 0 0 Updated Oct 9, 2020

• VEP_annotate

  CWL wrapper for VEP annotation
  Perl GPL-3.0 0 1 0 0 Updated Oct 7, 2020

• varscan_vcf_remap

  Modify fields of Varscan VCF files. CWL implementation
  Shell GPL-3.0 0 1 0 0 Updated Oct 5, 2020

• MergeFilterVCF

  CWL project for VCF merge and filter tool
  Shell GPL-3.0 0 0 0 0 Updated Oct 2, 2020

• WUDocker

  Utilities for launching docker in various Washington University environments
  Shell GPL-3.0 1 0 0 0 Updated Sep 29, 2020

• submit.CPTAC3

  Scripts for submission of CPTAC3 data
  Shell 1 0 0 0 Updated Sep 16, 2020

• cnvkit_pipeline

  call copy number from WES(WXS)
  Shell 1 1 0 0 Updated Sep 9, 2020

• SomaticSV

  CWL wrapper for Manta 1.4.0 and simple filter
  Shell GPL-3.0 1 3 0 0 Updated Aug 13, 2020

• HotspotFilter

  CWL implementation of filter which merges VCFs according to BED file
  Shell GPL-3.0 0 0 0 0 Updated Jul 22, 2020

• mnp_filter
  Python GPL-3.0 0 0 1 0 Updated Jul 21, 2020

• TinJasmine

  CWL germline variant caller
  Common Workflow Language GPL-3.0 0 0 0 0 Updated Jun 24, 2020