Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease

Docker Images

Pre-built Docker images are available on Docker Hub:

Environment	Tool	Pull Command
STAR	RNA-seq alignment	docker pull ashviyer/hd-ase-star
GATK	Variant calling	docker pull ashviyer/hd-ase-gatk
featureCounts	Read counting	docker pull ashviyer/hd-ase-featurecount
RSeQC	QC analysis	docker pull ashviyer/hd-ase-rseqc
pyNBS	Network clustering	docker pull ashviyer/hd-ase-pynbs

Run interactively:

docker run -it ashviyer/hd-ase-star

flowchart TD
    A[Processing RNA reads] --> B[WASP bias correction]
    B --> C[Variant Calling]
    C --> D[Allele specific expresssion counting]
    D --> E[Allele specific expression analysis ]
    E --> F[ASE based PPI network stratitification using pyNBS]
    F --> G[Compare clusters for significant allelic imbalance]
    F --> H[Compare clusters for significant dysregulated gene]
    G --> I[Identify key genes: Genes with both significant imbalance and gene expression change]
    H --> I[Identify key genes: Genes with both significant imbalance and gene expression change]
    I --> J[Extend key genes with known Huntington causative genes from DisGeNET]

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