Bioinformatics Tools and Applications for Transcriptomics and Chromatin Accessibility.

Bioinformatics is essential for life science, providing powerful tools to analyze and interpret complex biological data, driving discoveries and advancements in research. In this thesis it will be discussed the application of RNA-seq technology single cell analysis and the importance of statistical methods in such analysis (Ji & Sadreyev, 2018). I will present also two examples of the applications of RNAseq technology: - one in which RNA-seq was used to study proteomics(Challis et al., 2023) - and another in which scRNA-seq is integrated with ATAC-seq(Ranzoni et al., 2021) RNA-seq is a groundbreaking technology that enables comprehensive analysis of the transcriptome, capturing both qualitative and quantitative gene expression data. By sequencing all RNA molecules for each individual sample, RNA-seq reveals insights into gene regulation, alternative splicing, and cellular responses in unprecedented detail. However, extracting meaningful biological conclusions from this massive amount of data requires robust analytical approaches. Statistical tools play a crucial role in bioinformatics by enabling accurate interpretation of complex datasets, identifying significant patterns, and validating biological insights with confidence. Combining proteomics further strength the potentiality of scRNA-seq providing a powerful approach to link gene expression with protein function to uncover complex cellular mechanisms and to enhance our understanding of cellular heterogeneity.