Technology

Can differential expression methods developed originally for conventional bulk RNA-seq data also be applied to single-cell RNA-seq?

rna-seq

University of Turku researchers compared five statistical methods to detect differentially expressed genes between two distinct single-cell populations. Currently, it remains unclear whether differential expression methods developed originally for conventional bulk RNA-seq data can also be applied to single-cell RNA-seq ...

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aRNApipe – A balanced, efficient and distributed pipeline for processing RNA-seq data in high performance computing environments

rna-seq

The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. Researchers at the HudsonAlpha Institute for Biotechnology have developed aRNApipe, a project-oriented pipeline ...

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The Ensembl gene annotation system

rna-seq

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is ...

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multiDE – a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions

rna-seq

The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. Researchers at Fudan University have developed a novel method, multiDE, for facilitating DE analysis using RNA-seq read count data with ...

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