Tag Archives: Data Visualization

Heatmaps are an indispensible visualization tool for examining large-scale snapshots of genomic activity across various types of next-generation sequencing datasets. However, traditional heatmap software do not typically offer multi-scale insight across multiple layers of genomic analysis (e.g., differential expression analysis, ...

RNA-seq and similar methods can record gene expression within and among cells. Current methods typically lose positional information and many require arduous single-cell isolation and sequencing. A collaboration between professors Jonas Frisén (Karolinska Institutet) and Joakim Lundeberg (Royal Institute of ...

High-throughput single-cell technologies provide an unprecedented view into cellular heterogeneity, yet they pose new challenges in data analysis and interpretation. In this protocol, researchers from Stanford University describe the use of Spanning-tree Progression Analysis of Density-normalized Events (SPADE), a density-based ...

Researchers at the University of Miami Miller School of Medicine have developed a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of gene expression heatmaps, including integrated features to support: principal component analysis, differential expression analysis, gene ...

MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a ...

Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users ...

RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the massive amounts of data generated by large-scale RNA-seq remains a challenge. Multiple ...

Applications of deep-sequencing technologies in life science research and clinical diagnostics are rapidly expanding. Although fast data-processing algorithms exist, intuitive, portable data-evaluation solutions are still needed. Web tools have a history in bioinformatics of providing platform-independent, intuitive, barrier-free software solutions. ...

Canadian Bioinformatics Workshops – Informatics for RNA-sequence Analysis (QC) (2014) – Module 2 – RNA-seq alignment and visualization High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq ...

We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Pathway-based visualization is particularly powerful since it enables one to ...