Author

Tamsyn M. Crowley

Deakin UniversityORCID 0000-0002-3698-8917Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Assay:bulk RNA-seq· 4 Research Focus:benchmarking· 3 Research Focus:differential expression· 3 Approach:contrastive learning· 1 Research Focus:dimensionality reduction· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1

Frequent Co-Authors

Thomas P. QuinniD· 5 shared Mark F. RichardsoniD· 4 shared Ionas ErbiD· 2 shared Cédric NotredameiD· 1 shared David R. LovelliD· 1 shared Gregory Brian GlooriD· 1 shared Irva Hertz‐PicciottoiD· 1 shared Jerry LaiiD· 1 shared

Activity by Year

2017-2019 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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5 shared papersBioinformatics

Thomas P. QuinnORCID

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5 papers

Recent·Most cited

A field guide for the compositional analysis of any-omics data

Thomas P. Quinn, Ionas Erb, Gregory Brian Gloor, Cédric Notredame, Mark F. Richardson, Tamsyn M. Crowley

This paper provides a guide for applying compositional data analysis to NGS count data, emphasizing log-ratio transformations and addressing limitations of conventional normalization methods.

GigaScience · Sep 1, 2019Peer-reviewedBioinformatics

Solving for X: evidence for sex-specific autism biomarkers across multiple transcriptomic studies

Sam Lee, Thomas P. Quinn, Jerry Lai, Sek Won Kong, Irva Hertz‐Picciotto, Stephen J. Glatt, Tamsyn M. Crowley, Svetha Venkatesh, Thin Nguyen

This study identifies sex-dependent and -independent biomarkers in ASD using post-mortem brain RNA-Seq and blood microarray data, highlighting sex-specific gene expression differences and pathway dysregulation.

American Journal of Medical Genetics Part B Neuropsychiatric Genetics · Dec 6, 2018Peer-reviewedNeuroscience

Differential expression analysis of log-ratio transformed counts: benchmarking methods for RNA-Seq data

Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson

The paper benchmarks ALDEx2, a log-ratio transformation method, against conventional RNA-Seq differential expression tools, showing it has high precision and comparable performance on real data.

BMC Bioinformatics · Jul 18, 2018Peer-reviewedBioinformatics

Understanding sequencing data as compositions: anoutlook and review

Thomas P. Quinn, Ionas Erb, Mark F. Richardson, Tamsyn M. Crowley

This paper reviews compositional data analysis principles and discusses their application to sequencing data, highlighting challenges and future directions.

Bioinformatics · Mar 26, 2018Peer-reviewedBioinformatics

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

Thomas P. Quinn, Mark F. Richardson, David R. Lovell, Tamsyn M. Crowley

The paper introduces an R package for analyzing compositional data by implementing two proportionality measures and discussing their application to genomic data.

Scientific Reports · Nov 20, 2017Peer-reviewedBioinformatics