Blog

PhyLex

PhylEx: Clonal tree reconstruction via integration of bulk DNA-seq and scRNA-seq data

Seong-Hwan Jun

Revealing the evolutionary history of the cancer cells is challenging given the standard approach of single time point sequencing, as we cannot observe changes to cancer cells across time. This challenge has not deterred researchers from tackling the problem: using acute statistical models, researchers have developed methods to reconstruct clonal trees using only the cells sequenced at a single time point. In the early stages, the clone reconstruction approaches relied solely on the bulk DNA-seq data; however, with recent advances in single-cell technologies, it is now possible to resolve the ancestral structure with greater accuracy than ever before...

DataSpace MAb heatmap

New MAb Reports in DataSpace

Jason Taylor

Over the last year the DataSpace team has been working with researches and developers to redesign our data visualizations for monoclonal antibody data that is hosted in the application. The new reports offer a range of interactivity and a new visualization. In addition, the time the reports take to render in the browser has been greatly reduced, and data caps that were in place before have been removed. All plotting is now performed using JavaScript and the D3 JavaScript library which allows for a large decrease in rendering time and more flexibility in how plot elements appear in the application...

BayesSpace

BayesSpace - a tool for spatial transcriptomics analysis

Edward Zhao

In recent years, there has been rapid development of spatial gene expression technology. The most mature of these are the closely related Spatial Transcriptomics and Visium platforms from 10X Genomics, which allow for gene expression profiling to be done with morphological context. Already, these spatial technologies have shown promise to generate novel biological insights in diverse areas such as cancer immunology and prefrontal cortex cytoarchitecture. However, the spatial technology is limited to resolution on the order of 10 cells per spot (the unit of observation for these data). In the meantime, development of analytical tools that effectively utilize the available spatial information and enhance the gene expression maps to higher resolution have lagged behind...