Background: Single-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches. Results: Autoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions. Conclusions: scAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics.
Tangherloni, A., Ricciuti, F., Besozzi, D., Lio, P., & Cvejic, A. (2021). Analysis of single-cell RNA sequencing data based on autoencoders. BMC BIOINFORMATICS, 22(1) [10.1186/s12859-021-04150-3].
|Citazione:||Tangherloni, A., Ricciuti, F., Besozzi, D., Lio, P., & Cvejic, A. (2021). Analysis of single-cell RNA sequencing data based on autoencoders. BMC BIOINFORMATICS, 22(1) [10.1186/s12859-021-04150-3].|
|Tipo:||Articolo in rivista - Articolo scientifico|
|Carattere della pubblicazione:||Scientifica|
|Presenza di un coautore afferente ad Istituzioni straniere:||Si|
|Titolo:||Analysis of single-cell RNA sequencing data based on autoencoders|
|Autori:||Tangherloni, A; Ricciuti, F; Besozzi, D; Lio, P; Cvejic, A|
TANGHERLONI, ANDREA (Corresponding)
|Data di pubblicazione:||2021|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1186/s12859-021-04150-3|
|Appare nelle tipologie:||01 - Articolo su rivista|