Tag Archives: Data Visualization

RNA-sequencing (RNA-seq) and microarrays are methods for measuring gene expression across the entire transcriptome. Recent advances have made these techniques practical and affordable for essentially any laboratory with experience in molecular biology. A variety of computational methods have been developed ...

Single cell RNA-seq (scRNA-seq) experiments can provide a wealth of information about heterogeneous, multi-cellular systems. However, this information has to be inferred computationally from sequencing reads which constitute a sparse and noisy sub-sampling of the actual cellular transcriptomes. Here, University ...

Prior publications in the biological heatmap visualization field have focused predominantly on the production of static heatmaps, which do not constitute a computational challenge and are relatively simple to make using limited computational resources. In contrast, interactive heatmaps present a ...

Sequencing of transcribed RNA molecules (RNA-seq) has been used wildly for studying cell transcriptomes in bulk or at the single-cell level and is becoming the de facto technology for investigating gene expression level changes in various biological conditions, on the ...

Grade of membership models, also known as “admixture models”, “topic models” or “Latent Dirichlet Allocation”, are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to ...

10x Genomics, a company focused on enabling the mastery of biology by accelerating genomic discovery, today announced the launch of a new software suite for analyzing and visualizing single-cell RNA sequencing (scRNA-seq) data generated by the company’s Chromium™ Single Cell ...

Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or ...

RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and ...

The increasing amount of heterogeneous Next Generation Sequencing (NGS) data generated today necessitates a robust platform for the efficient data storage, management, pre-processing, quality checking, analysis and visualization. Addressing each of these categories is a tremendous undertaking requiring high-level expertise ...

Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA ...