Tag Archives: Reproducibility

The pandemic has shown that scientists across the globe are willing to join forces to better understand the virus and to develop new treatments and vaccines. Key scientific achievements in this respect – some of them already in the early ...

Ribonucleic acid sequencing (RNA-seq) identifies and quantifies RNA molecules from a biological sample. Transformation from raw sequencing data to meaningful gene or isoform counts requires an in...

A necessary pre-processing data analysis step is the removal of adapter sequences from the raw reads. While most adapter trimming tools require adapter sequence as an essential input, adapter information is often incomplete or missing. This can impact quantification of ...

From 2019-09-08 to 2019-09-08 - In this training course, we provide a summary of the applications of Next Generation Sequencing (NGS) technologies in the clinical context. These are presented through a hands-on session on RNA-Seq data analysis, following...

The development of high-throughput experimental technologies, such as next-generation sequencing, have led to new challenges for handling, analyzing and integrating the resulting large and diverse datasets. Bioinformatical analysis of these data commonly requires a number of mutually dependent steps applied ...

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. University of Washington, Tacoma researchers describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. They provide a user-friendly tool, ...

Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to ...

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 ...

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented ...

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the ...