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Shiny app for exploring vascular endothelial cell genomics database
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ATAC_principalComponents.rds
ATAC_principalComponents_differentialPeaks.rds
AdultBrainEC_intersect_DEG.rds
BBB_genes.rds
BBB_genes_lost.rds
BrainEC_intersect_DEG.rds
CulturedEC_intersect_DEG.rds
DMR_methyl_highVariance_motifs.rds
DMR_methyl_principalComponents.rds
EC_TPMs.rds
EC_TPMs_averages copy.rds
EC_TPMs_averages.rds
EC_TPMs_tidy.rds
EC_enriched_transcripts.rds
KidneyEC_intersect_DEG.rds
LICENSE
LiverEC_intersect_DEG.rds
LungEC_intersect_DEG.rds
P7_specific_DEG.rds
README.md
app.R
endothelial_dat_summary.rds
endothelial_scaled_summary.rds
gene_list.rds
highVariance_motifs.rds
highVariance_motifs_differentialPeaks.rds
methyl_highVariance_motifs.rds
methyl_principalComponents.rds
pan_endothelial_genes.rds

README.md

Vascular Endothelial Cell Trans-omics Resource Database (VECTRDB)

This Shiny App will allow you to explore the Vascular Endothelial Cell Trans-omics Resource Database (VECTRDB), a database that integrates and compares the transcriptional, chromatin accessibility, and DNA methylation landscapes of vascular endothelial cells (ECs). Unbiased RNA-seq, ATAC-seq, and MethylC-seq enabled exploration of these landscapes among postnatal day 7 (P7) vascular ECs isolated from brain, liver, lung, and kidney of Tie2-GFP transgenic mice. These datasets should provide a foundation to determine the factors that are associated with EC heterogeneity. The app also allows exploration of EC gene expression in the developing CNS at single cell resolution.

The app is also accessible via https://markfsabbagh.shinyapps.io/vectrdb/

Running the app locally

To use the app on your local computer, simply run the following commands from an R console:

install.packages("shiny")
library(shiny)
runGitHub("EC_Genomics","mfsabbagh")

Citation

Please cite as: Mark F. Sabbagh, Jacob S. Heng, Chongyuan Luo, Rosa G. Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, and Jeremy Nathans. "Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells." eLife 2018;7:e36187 DOI: 10.7554/eLife.36187

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