Analysis Pipelines

To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users...

Over the past two decades, researchers have discovered a special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs (circRNAs) have garnered considerable...

Single-cell RNA sequencing (scRNA-seq) can map cell types, states and transitions during dynamic biological processes such as tissue development and regeneration. Many trajectory inference methods have been developed to order cells by their progression...

We hope that SCAN-B RNA sequencing will be in clinical use as early as next year, mainly to help in the identification of which breast tumours are...

With new technological developments, the number of sequencing applications is continuously expanding, while at the same time sequencing prices are falling. This is resulting in an exponential increase in sequencing data. However, while ‘big data’ brings more...

Transposable elements (TEs) are mobile genetic elements in eukaryotic genomes. Recent research highlights the important role of TEs in the embryogenesis, neurodevelopment, and immune functions...

University of Zürich researchers have developed pipeComp, a flexible R framework for pipeline comparison handling interactions between analysis steps and relying on multi-level evaluation metrics. The researchers apply it to the benchmark of single-cell RNA...

Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of ...

Stratification of breast cancer (BC) into molecular subtypes by multigene expression assays is of demonstrated clinical utility. In principle, global RNA-sequencing (RNA-seq) should enable reconstructing existing transcriptional classifications of BC samples. Yet, it is not clear whether adaptation to RNA-seq ...

MicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs...