Repositories list

• PCAP-core

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

  legacy-supportpcapperl+ 1icgc

  Perl

  •

  GNU General Public License v2.0

  •14•13•1•1•Updated Jun 12, 2024Jun 12, 2024

• TumorType-WGS

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

  R

  •

  Apache License 2.0

  •22•46•4•0•Updated Nov 20, 2023Nov 20, 2023

• Seqware-BWA-Workflow

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

  Perl

  •

  GNU General Public License v3.0

  •11•11•7•1•Updated Dec 27, 2022Dec 27, 2022

• pcawg3-transcriptome-integration

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

  R

  •0•1•0•0•Updated Jul 25, 2022Jul 25, 2022

• pcawg3-transcriptome-expression

  Public
  Code used for generating expression counts

  Shell

  •0•0•0•0•Updated Feb 7, 2022Feb 7, 2022

• pcawg3-rnaseq-align-star

  Public
  Scripts for RNA-Seq alignments using STAR

  Python

  •

  MIT License

  •1•6•0•0•Updated Feb 7, 2022Feb 7, 2022

• demo-pkgs2

  Public archive
  Nextflow

  •

  MIT License

  •2•0•0•0•Updated Aug 25, 2021Aug 25, 2021

• demo-pkgs1

  Public archive
  Nextflow

  •

  MIT License

  •2•0•0•0•Updated Aug 25, 2021Aug 25, 2021

• pcawg-metadata

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

  Python

  •2•0•0•0•Updated Mar 17, 2021Mar 17, 2021

• CGP-Somatic-Docker

  Public
  Dockerised and simplified version of SeqWare-CGP-SomaticCore

  Java

  •

  GNU Affero General Public License v3.0

  •9•14•2•0•Updated Mar 5, 2021Mar 5, 2021

• awesome-wfpkgs2

  Public
  Nextflow

  •

  MIT License

  •0•2•0•0•Updated Feb 21, 2021Feb 21, 2021

• awesome-wfpkgs1

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Feb 21, 2021Feb 21, 2021

• demo-wfs

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Feb 16, 2021Feb 16, 2021

• demo-wf-pkgs

  Public
  0•0•0•0•Updated Feb 1, 2021Feb 1, 2021

• demo-tool-pkgs

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Feb 1, 2021Feb 1, 2021

• pcawg3-transcriptome-splicing

  Public
  This repository contains code for the alternative splicing analysis of the PCAWG Transcriptome working group (PCAWG3)

  Python

  •0•6•0•0•Updated Feb 5, 2020Feb 5, 2020

• pcawg_delly_workflow

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

  Python

  •8•18•4•0•Updated Jan 22, 2020Jan 22, 2020

• pcawg3-alternative-promoter

  Public
  The PCAWG3 alternative promoter pipeline

  R

  •1•2•0•0•Updated Jun 27, 2019Jun 27, 2019

• pcawg3_germline_qtl

  Public
  Python

  •0•1•0•0•Updated Jun 6, 2019Jun 6, 2019

• dkfz_dockered_workflows

  Public
  This is the container that houses the Roddy-based component provided by DKFZ for the DEWrapper workflow

  Shell

  •5•9•7•0•Updated May 14, 2019May 14, 2019

• pcawg-muse

  Public
  Python

  •7•0•0•0•Updated May 14, 2019May 14, 2019

• pcawg-ega-submission

  Public
  Git repository for tracking PCAWG data submission to EGA

  Shell

  •3•0•0•0•Updated Mar 26, 2019Mar 26, 2019

• pcawg-minibam

  Public
  bamcwlpcawg+ 3minibamvariantbamcwl-workflow

  JavaScript

  •2•1•0•1•Updated Dec 28, 2018Dec 28, 2018

• OxoG-Dockstore-Tools

  Public
  A CWL version of the Seqware OxoG workflow. This repository also contains scripts and dockerfiles used by the stand-alone versions of these components.

  pcawgoxog-filteringsnv-annotation+ 3indel-annotationminibamcwl

  Shell

  •6•4•0•0•Updated Nov 30, 2018Nov 30, 2018

• pcawg3-ase-sigqtl

  Public
  R

  •0•1•0•0•Updated Nov 23, 2018Nov 23, 2018

• minibam-icgc-generator-jt

  Public
  Python

  •0•0•1•0•Updated Oct 3, 2018Oct 3, 2018

• oxog-ops

  Public
  Github repo for scheduling and tracking OxoG workflow jobs

  Perl

  •1•0•0•0•Updated Sep 28, 2018Sep 28, 2018

• GA4GH-DREAM_Workflow_Execution_Challenge

  Public
  Repository for staging PCAWG workflows into GA4GH-DREAM Workflow Execution Challenge

  Shell

  •0•0•1•0•Updated Sep 13, 2018Sep 13, 2018

• pcawg-workflow-runner-jt

  Public
  JTracker workflow to run PCAWG workflow with data provisioning support

  Python

  •1•0•0•0•Updated May 9, 2018May 9, 2018

• pcawg-snv-indel-annotation

  Public
  This workflow performs annotation on SNV and INDEL VCFs.

  cwlpcawgsnv-annotation+ 2indel-annotationcwl-workflow

  JavaScript

  •0•4•1•1•Updated Feb 5, 2018Feb 5, 2018