Repositories list

• vcfqc

  Public
  MIT License

  •0•0•0•1•Updated Feb 12, 2025Feb 12, 2025

• argo-modules

  Public
  ARGO specific modules using nf-core framework

  HTML

  •

  MIT License

  •0•0•3•5•Updated Feb 11, 2025Feb 11, 2025

• prealnqc

  Public
  Python

  •

  MIT License

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

• dnaalnqc

  Public
  ICGC-ARGO workflow for DNA-Seq alignment QC

  mupad

  •

  MIT License

  •1•4•1•0•Updated Nov 20, 2024Nov 20, 2024

• target_seq_bed_files

  Public
  A repository to capture genes targeted by WES and target-Seq from ICGC-ARGO projects

  MIT License

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

• icgc-argo-mutational-signatures

  Public
  ICGC ARGO Mutational Signatures Workflow Packages

  Nextflow

  •

  MIT License

  •0•2•0•0•Updated Oct 28, 2024Oct 28, 2024

• vcf-annotation

  Public
  ICGC ARGO Workflow for VCF Annotation

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• xml_variant_ingestion

  Public
  ICGC ARGO variant calling pipeline which digest xml to vcf variant format

  Nextflow

  •

  GNU Affero General Public License v3.0

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

• rnaaln

  Public
  ICGC ARGO Workflow for RNA-Seq Alignment

  GNU Affero General Public License v3.0

  •0•0•0•1•Updated Sep 23, 2024Sep 23, 2024

• dnaaln

  Public
  ICGC ARGO Workflow for DNA-Seq Alignment

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

• dna-seq-processing-wfs

  Public
  ICGC ARGO DNA-Seq Processing Workflow

  workflowbioinformaticscancer-genomics+ 2dna-seqnextflow

  Nextflow

  •

  GNU Affero General Public License v3.0

  •4•5•2•0•Updated Jul 23, 2024Jul 23, 2024

• argo-reference-files

  Public
  Reference files used by the ICGC-ARGO data analysis pipelines

  GNU Affero General Public License v3.0

  •0•0•1•0•Updated Jul 3, 2024Jul 3, 2024

• rna-seq-alignment

  Public
  RNA-Seq alignment packages

  Nextflow

  •

  MIT License

  •1•5•0•0•Updated Apr 18, 2024Apr 18, 2024

• sanger-wgs-variant-calling

  Public
  ICGC-ARGO Sanger WGS Somatic Variant Calling Workflow

  workflowbioinformaticsgenomics+ 1cancer

  Nextflow

  •

  GNU Affero General Public License v3.0

  •3•4•3•0•Updated Mar 26, 2024Mar 26, 2024

• rna-seq-expression-counting

  Public
  Nextflow

  •

  MIT License

  •0•1•0•0•Updated Jan 2, 2024Jan 2, 2024

• germlinevar

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jun 30, 2023Jun 30, 2023

• open-access-variant-filtering

  Public
  Nextflow

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Jun 29, 2023Jun 29, 2023

• gatk-mutect2-variant-calling

  Public
  ICGC ARGO GATK Mutect2 Somatic Variant Calling Workflow

  workflowbioinformaticsgenomics+ 1cancer

  Nextflow

  •

  GNU Affero General Public License v3.0

  •2•0•1•0•Updated Jun 29, 2023Jun 29, 2023

• sanger-wxs-variant-calling

  Public
  ICGC-ARGO Sanger WXS Somatic Variant Calling Workflow

  workflowbioinformaticsgenomics+ 1cancer

  Nextflow

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Jun 29, 2023Jun 29, 2023

• data-processing-utility-tools

  Public
  Collection of utility tools for ARGO data processing

  Python

  •

  GNU Affero General Public License v3.0

  •2•0•0•0•Updated Jun 8, 2023Jun 8, 2023

• nextflow-data-processing-utility-tools

  Public
  Nextflow implementation of https://github.com/icgc-argo/data-processing-utility-tools

  Nextflow

  •

  Apache License 2.0

  •1•0•2•0•Updated May 30, 2023May 30, 2023

• ase

  Public
  ICGC-ARGO pipeline for analysis of allele specific expression (ASE) based on RNA-seq data

  0•0•0•0•Updated May 2, 2023May 2, 2023

• pre-alignment-qc

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Mar 9, 2023Mar 9, 2023

• rna-seq-data-simulation

  Public
  Data simulation scripts for RNA-Seq working group

  Python

  •0•0•0•0•Updated Nov 3, 2022Nov 3, 2022

• allele-specific-expression

  Public
  Allele Specific Expression (ASE) analysis package

  Python

  •

  MIT License

  •1•4•0•0•Updated Aug 16, 2022Aug 16, 2022

• argo-qc-tools

  Public
  Collection of ARGO data quality tool packages

  HTML

  •

  MIT License

  •1•1•0•0•Updated Jun 28, 2022Jun 28, 2022

• dna-seq-processing-tools

  Public
  A collection of DNA processing tools / modules used in the ICGC ARGO alignment workflow

  workflowbioinformaticsgenomics+ 1cancer

  Python

  •

  GNU Affero General Public License v3.0

  •1•3•1•0•Updated Jun 23, 2022Jun 23, 2022

• gatk-rna-mutect2-variant-calling

  Public
  GATK Variant Calling for RNA-Seq

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated May 26, 2022May 26, 2022

• argo-analysis-pipelines-overview

  Public
  Overview of ICGC-ARGO Analysis Pipelines

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated May 18, 2022May 18, 2022

• metadata-for-benchmarking-datasets

  Public
  This repository contains metadata information for PCAWG WGS/RNA-Seq/Validation datasets

  Python

  •2•1•0•0•Updated May 13, 2022May 13, 2022