Project Contacts

For further information about this project, please contact:

• Dr Dean Thompson (dean.thompson@newcastle.ac.uk)
• Dr Ruth Cranston (ruth.cranston@newcastle.ac.uk)

Project Description

Clinical trials 'omics data processing. This currently includes (but is not limited to): RNA-Sequencing, DNA Methylation, Long Read Sequencing, Mutation Panels.

Software or Compute Methods

Analytical pipelines include software for:



Raw Data QC (MultiQC, FastQC, Trim Galore!),

Alignment (Bismark, HTSeq, salmon, kallisto ...),

Deduplication (GATK),

RNA read counts generation, fusion analysis (arriba, cicero),

GATK 4.0 based analyses (Mutect).

AI-based image analysis (python based, torchvision, tensorflow, scikit-learn, scikit-image)