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ICGC-TCGA-PanCancer

ICGC-TCGA-PanCancer

Geek Repo

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

Home Page:http://pancancer.info

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ICGC-TCGA-PanCancer's repositories

TumorType-WGS

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

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pcawg_delly_workflow

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

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CGP-Somatic-Docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore

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PCAP-core

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

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Seqware-BWA-Workflow

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

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dkfz_dockered_workflows

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

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pcawg3-rnaseq-align-star

Scripts for RNA-Seq alignments using STAR

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pcawg3-transcriptome-splicing

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

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OxoG-Dockstore-Tools

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

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pcawg-snv-indel-annotation

This workflow performs annotation on SNV and INDEL VCFs.

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awesome-wfpkgs2

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pcawg3-alternative-promoter

The PCAWG3 alternative promoter pipeline

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pcawg-minibam

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pcawg3-ase-sigqtl

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pcawg3-transcriptome-integration

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

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pcawg3_germline_qtl

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awesome-wfpkgs1

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demo-pkgs1

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demo-pkgs2

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demo-tool-pkgs

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demo-wf-pkgs

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demo-wfs

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GA4GH-DREAM_Workflow_Execution_Challenge

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

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minibam-icgc-generator-jt

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oxog-ops

Github repo for scheduling and tracking OxoG workflow jobs

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pcawg-ega-submission

Git repository for tracking PCAWG data submission to EGA

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pcawg-metadata

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

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pcawg-muse

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pcawg-workflow-runner-jt

JTracker workflow to run PCAWG workflow with data provisioning support

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pcawg3-transcriptome-expression

Code used for generating expression counts

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