PlaqView-ATAC

Instructions:

Select a dataset from the BLUE drop-down Menu.
Click the blue 'Load Dataset' button.
The 'Start Exploring' button will appear when data is loaded.
(Optional) come back to this page to load another dataset.

Select a Dataset

About Us

This interactive web application is designed for lay scientists to explore complex single-cell ATAC-seq dataset from human and mouse cardiovascular tissues.

PlaqView is officially published at Atherosclerosis!

Please cite PlaqView if you find us helpful. Submit your data to us at plaqview@virginia.edu.

Details of Single- Cell Dataset and IDs

Query Gene Expression

please follow HUGO conventions

Select Labeling Method

Gene Score Prediction Method

Gene Expression Score Predictor

Use this module to query specific gene(s) and generate graphs for publications.

By default, for scATAC-seq datasets, PlaqView uses ArchR's to predict gene scores based on nearby open regions. Details for this calculation can be found on this page.

In short, a gene score is essentially a prediction of how highly expressed a gene will be based on the accessibility of regulatory elements in the vicinity of the gene. ArchR also uses MAGIC to imputes the gene scores by smoothing the signal across genes.

Download UMAP

Download Expression Plot

Top Significantly Enriched Pathways

You must restart query if you change database Download Complete Pathway Enrichment Data

Query Chromatin Tracks

please follow HUGO conventions

Select Labeling Method

Peak2Gene Overlay

Genome Track Browser

Use this module to query specific gene(s) and generate graphs for publications.

In addition to calculating gene scores, PlaqView can also visualize the nearby chromatin accessibility, as powered by ArchR. Details for this visualization can be found here.