Repositories list

• TypeSeq2

  Public
  R

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

• GwasQcPipeline

  Public
  The CGR GWAS QC processing workflow.

  gwasplinkcancer-genomics+ 2illumina-bead-chipsnakemake

  Python

  •

  MIT License

  •3•0•21•1•Updated Oct 31, 2024Oct 31, 2024

• GenCompass_WGS

  Public
  GenCompass: Germline Ensemble Calling of Mutations with Parabricks Accelerated Software Suite

  Python

  •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• ExomeQcPipeline

  Public
  Python

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

• GwasQcPipeline-test-data

  Public
  Fake test data sets for the GwasQcPipeline.

  Shell

  •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

• ImpureMerge

  Public
  Python

  •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

• TriosCompass_v2

  Public
  Trios analysis workflow written in Snakemake

  HTML

  •

  MIT License

  •0•0•0•1•Updated Sep 13, 2024Sep 13, 2024

• MineSV

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Sep 10, 2024Sep 10, 2024

• PreImputePipeline

  Public
  PreImputePipeline

  C++

  •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

• PLP_prediction_workflow

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• gatk-sv

  Public
  A structural variation pipeline for short-read sequencing - modified to run on HPC

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •71•0•1•0•Updated May 28, 2024May 28, 2024

• GEMSCAN

  Public
  Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

  variant-callingdeepvariantworkflow+ 3snakemakestrelka2gatk4-haplotypecaller

  Python

  •

  MIT License

  •8•7•15•0•Updated May 1, 2024May 1, 2024

• UKB_extract_variants

  Public
  Extract variants of interest from UKB Biobank data hosted at DNAnexus

  Perl

  •

  MIT License

  •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024

• conda-cgr

  Public
  CGR conda channel

  HTML

  •1•1•3•0•Updated Apr 25, 2024Apr 25, 2024

• HPV_low_VAF_SNV_prediction

  Public
  Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning

  machine-learningvcfcancer-genomics+ 14variant-callingsnvvcf-filesngs-analysishpvion-torrentvariant-call-format+ 7

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 12, 2024Mar 12, 2024

• Gencode_microRNA-seq

  Public
  microRNA-seq workflow utilizing STAR to generate a Sample-Gene read count matrix

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•6•0•Updated Jan 5, 2024Jan 5, 2024

• IlluminaSequencingAnalysis

  Public
  All Illumina Sequencing Related project from Xin will be recorded in this repo

  Shell

  •0•0•60•0•Updated Dec 21, 2023Dec 21, 2023

• igv_snapshot_maker

  Public
  Perl

  •

  MIT License

  •0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

• CGR_pacbio_hpylori_analysis_pipeline

  Public
  Shell

  •0•0•0•0•Updated Sep 1, 2023Sep 1, 2023

• QIIME_pipeline

  Public
  CGR's QIIME microbiome pipeline

  Python

  •

  MIT License

  •3•3•1•0•Updated Aug 10, 2023Aug 10, 2023

• HPVMethyl

  Public
  R

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• TypeSeqHPV

  Public
  NCI CGR laboratory HPV typing analysis workflows

  dockerrtidyverse+ 2ion-torrent-plugintorrent-server

  R

  •4•5•0•0•Updated Dec 15, 2022Dec 15, 2022

• somatic-conda

  Public
  This is a full snakemake pipeline for somatic-combiner.

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 20, 2022Sep 20, 2022

• annotate_rsids_from_linker

  Public
  Use linker file to map chr:pos to rsID labels, for plco-analysis

  M4

  •

  MIT License

  •0•0•0•0•Updated Jan 16, 2022Jan 16, 2022

• annotate_frequency

  Public
  Annotate plco-analysis intermediate files with frequency data

  M4

  •

  MIT License

  •0•0•0•0•Updated Dec 24, 2021Dec 24, 2021

• RNA_CGR_Pipeline

  Public
  The RNA pipeline developed by Mia and Xin, including RNA analysis pipeline and RNA auto-launcher

  Python

  •

  MIT License

  •1•0•0•0•Updated Dec 14, 2021Dec 14, 2021

• plco-analysis

  Public
  Primary workflow for the PLCO "Atlas" project

  Shell

  •4•3•10•0•Updated Dec 14, 2021Dec 14, 2021

• COVNET-GWAS

  Public
  COVNET GWAS pipeline developement

  BSD 3-Clause "New" or "Revised" License

  •1•0•1•1•Updated Dec 9, 2021Dec 9, 2021

• Nanopore_Pore_C_Tips

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

• PING_BIOWULF

  Public
  A workflow to run PING (Pushing Immunogenetics to the Next Generation) efficiently on NIH Biowulf

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 24, 2021Sep 24, 2021