Personalised ASE Caller (PAC): Software for better alignment of RNA sequencing data for use in allele specific expression analysis.

 

The method is described here: Saukkonen, A., Kilpinen, H., & Hodgkinson, A. 2022. Highly accurate quantification of allelic gene expression for population and disease genetics. Genome Research. gr.276296.121.

 

Software and guidance on usage: HERE

 

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MitoNuclearCOEXPlorer: Analysis of gene expression interactions involving the mitochondrial and nuclear genomes.

 

The method is described here: Fairbrother-Browne, A., Ali, A., Reynolds, R., Garcia-Ruiz, S., Zhang, D., Chen, Z., Ryten, M. and Hodgkinson, A. 2021, Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease. Communications Biology 4: 1262.

 

 Software and guidance on usageHERE

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MitoRNACleave: A method for detecting mitochondrial RNA cleavage sites from short read sequencing data.

The method is described here: Antona, G-C, Ali, A.T., Hodgkinson, A. 2022. Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors. BMC Biology 20:168.

 Software and guidance on usage: HERE

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ASE Detector: Software for better alignment of RNA sequencing data for use in allele specific expression analysis.

The method is described here: Hodgkinson, A., Grenier, J. C., Gbeha, E., & Awadalla, P. 2016. A haplotype-based normalization technique for the analysis and detection of allele specific expression. BMC Bioinformatics 17: 364. 

 Software and guidance on usage: HERE