Transmorph: a unifying computational framework for modular single-cell RNA-seq data integration

Abstract

Data integration of single-cell RNA-seq (scRNA-seq) data describes the task of embedding datasets gathered from different sources or experiments into a common representation so that cells with similar types or states are embedded close to one another independently from their dataset of origin. Data integration is a crucial step in most scRNA-seq data analysis pipelines involving multiple batches. It improves data visualization, batch effect reduction, clustering, label transfer, and cell type inference. Many data integration tools have been proposed during the last decade, but a surge in the number of these methods has made it difficult to pick one for a given use case. Furthermore, these tools are provided as rigid pieces of software, making it hard to adapt them to various specific scenarios. In order to address both of these issues at once, we introduce the transmorph framework. It allows the user to engineer powerful data integration pipelines and is supported by a rich software ecosystem. We demonstrate transmorph usefulness by solving a variety of practical challenges on scRNA-seq datasets including joint datasets embedding, gene space integration, and transfer of cycle phase annotations. transmorph is provided as an open source python package.

Evaluating batch correction methods for image-based cell profiling

“…No systematic and comprehensive comparison and evaluation of such methods has been performed, making it unclear whether the available methods offer a reliable approach for dealing with batch effects in image-based profiling. Evaluations on single- cell RNA-seq (scRNA-seq) batch correction methods reveal that no one method consistently outperforms the others 14,15 and suggest that most of these methods should not be used without the guidance of an expert 16,17 . Therefore, it remains unknown whether any of the scRNA-seq batch correction methods can be reliably applied to image-based profiles.…”