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@ICGC-TCGA-PanCancer

ICGC-TCGA-PanCancer

This collection of repositories were developed for the purpose of processing data for the PanCancer project.

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  1. TumorType-WGS TumorType-WGS Public

    Classifying tumor types based on Whole Genome Sequencing (WGS) data

    R 46 22

  2. pcawg_delly_workflow pcawg_delly_workflow Public

    A mirror of https://bitbucket.org/weischen/pcawg-delly-workflow

    Python 18 8

  3. CGP-Somatic-Docker CGP-Somatic-Docker Public

    Dockerised and simplified version of SeqWare-CGP-SomaticCore

    Java 14 9

  4. PCAP-core PCAP-core Public

    Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

    Perl 13 14

  5. Seqware-BWA-Workflow Seqware-BWA-Workflow Public

    This is the BWA workflow used in the PanCancer project used to allign all the BAM files.

    Perl 11 11

  6. pcawg-colour-palette pcawg-colour-palette Public

    For mapping terms to standardized colours

    R 10 2

Repositories

Showing 10 of 81 repositories
  • PCAP-core Public

    Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

    ICGC-TCGA-PanCancer/PCAP-core’s past year of commit activity
    Perl 13 GPL-2.0 14 1 1 Updated Jun 12, 2024
  • TumorType-WGS Public

    Classifying tumor types based on Whole Genome Sequencing (WGS) data

    ICGC-TCGA-PanCancer/TumorType-WGS’s past year of commit activity
    R 46 Apache-2.0 22 4 0 Updated Nov 20, 2023
  • Seqware-BWA-Workflow Public

    This is the BWA workflow used in the PanCancer project used to allign all the BAM files.

    ICGC-TCGA-PanCancer/Seqware-BWA-Workflow’s past year of commit activity
    Perl 11 GPL-3.0 11 7 1 Updated Dec 27, 2022
  • pcawg3-transcriptome-integration Public

    Code for the integration of all transcriptomic abberations of the PCAWG Transcriptome working group (PCAWG3)

    ICGC-TCGA-PanCancer/pcawg3-transcriptome-integration’s past year of commit activity
    R 1 0 0 0 Updated Jul 25, 2022
  • pcawg3-transcriptome-expression Public

    Code used for generating expression counts

    ICGC-TCGA-PanCancer/pcawg3-transcriptome-expression’s past year of commit activity
    Shell 0 0 0 0 Updated Feb 7, 2022
  • pcawg3-rnaseq-align-star Public

    Scripts for RNA-Seq alignments using STAR

    ICGC-TCGA-PanCancer/pcawg3-rnaseq-align-star’s past year of commit activity
    Python 6 MIT 1 0 0 Updated Feb 7, 2022
  • demo-pkgs2 Public archive Forked from icgc-argo-workflows/demo-pkgs2
    ICGC-TCGA-PanCancer/demo-pkgs2’s past year of commit activity
    Nextflow 0 MIT 2 0 0 Updated Aug 25, 2021
  • demo-pkgs1 Public archive Forked from icgc-argo-workflows/demo-pkgs1
    ICGC-TCGA-PanCancer/demo-pkgs1’s past year of commit activity
    Nextflow 0 MIT 2 0 0 Updated Aug 25, 2021
  • pcawg-metadata Public Forked from icgc-argo-workflows/metadata-for-benchmarking-datasets

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

    ICGC-TCGA-PanCancer/pcawg-metadata’s past year of commit activity
    Python 0 2 0 0 Updated Mar 17, 2021
  • CGP-Somatic-Docker Public

    Dockerised and simplified version of SeqWare-CGP-SomaticCore

    ICGC-TCGA-PanCancer/CGP-Somatic-Docker’s past year of commit activity
    Java 14 AGPL-3.0 9 2 0 Updated Mar 5, 2021
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