Bioinformatics Seminar
Time: 11AM
Venue: Hybrid
11 July 2023
mastR: an Automated Marker Screening Tool in R
Jinjin ChenWEHI Bioinformatics
Marker genes are important in biological and medical research, playing a significant role in advancing knowledge and applications across various fields as they can help diagnose, monitor, and treat diseases. They exhibit specificity towards a particular group or condition of interest in the biology and can be identified through various methods, such as transcriptomics, proteomics, or metabolomics. To denote these marker genes, we use the term 'group markers' in a generic sense. In most cases, markers identification has a few limitations. Firstly, most of these methods ignore the background expression of the context. Secondly, the required manual curation of markers by experts is a time-consuming and labour-intensive process. Thirdly, existing marker identification methods primarily focus on single-cell RNA-sequencing (scRNA-seq) data, leaving a critical gap for marker identification in bulk RNA-sequencing data. To address these challenges, I developed mastR, a novel approach that overcomes these limitations and achieves high performance on both simulated and real data. mastR provides a comprehensive solution for marker identification, specifically tailored for bulk RNA-sequencing data. By considering background expression and implementing advanced algorithms, mastR offers a robust and efficient method for accurate marker identification.