In one of my last blog posts I talked about Periscope which is a new R package to assist with creating shiny applications. We have been improving the package lately with a couple of items like support for row names in the DataTable module and a gallery page with periscope apps. Feel free to add your awesome application to the gallery page as well! These are the current applications.
Single Cell Viewer
Thanks to technological advances made in the last few years, we are now able to study transcriptomes from thousands of single cells. These have been applied widely to study various aspects of Biology. Nevertheless, comprehending and inferring meaningful biological insights from these large datasets is still a challenge. Although tools are being developed to deal with the data complexity and data volume, we do not have yet an effective visualizations and comparative analysis tools to realize the full value of these datasets.
In order to address this gap, we implemented a single cell data visualization portal called Single Cell Viewer (SCV). SCV is an R shiny application that offers users rich visualization and exploratory data analysis options for single cell datasets.
Interactive Gene explorer
IPF (Idiopathic Pulmonary Fibrosis) is a fatal disease that usually affects adults between the ages of 50-70. The disease is characterized by progressive decline in lung function resulting from scarring of lung tissue. With certain treatments, the disease progress might be stopped. In the dataset for the application, scientists have been looking at TGFb treatment and the results in gene expression.
The shiny application that has been developed can be used to gain insights from the research data.
The dataset is divided into 9 contrasts, each containing (the same) 100 Genes. The first tab displays the Genes per contrasts and per gene the average gene expression, the (log) fold change and the P values. In the second tab, the treatment group vs the gene’s log2CPM value is shown. In the third tab, the data is displayed in a data table.
Periscope sample application
Sample shiny application demonstrating the functionality of the periscope framework. This is very useful if you are starting with the periscope package and want to explore the functionality.