Shiny apps from the Bader Lab

Welcome to the Bader Lab’s home for all things (R)Shiny!

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Mouse Retinal Stem Cells

Data portal for the paper A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells by Coles, Labib, et al. Lab on a Chip, 2021. This is an RShiny app based on scClustViz for exploring the single-cell transcriptomes of cells isolated from the mouse retina and enriched for stem cells using the published microfluidics platform.

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Aging Mouse Brain

Data portal for the paper Single-cell transcriptomic profiling of the aging mouse brain by Ximerakis, Lipnick, et al. Nat Neurosci, 2019. This data portal includes RShiny apps based on both scClustViz for exploring scRNAseq data and CCInx for predicting interactions between cell types.

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hPSC-derived LSECs

Data portal for the paper Generation of functional liver sinusoidal endothelial cells from human pluripotent stem-cell-derived venous angioblasts by Gage et al. Cell Stem Cell, 2020. This data portal includes RShiny apps based on scClustViz for exploring scRNAseq data of hPSC-derived LSECs generated from the maturation of venous angioblasts in NSG mice, as well as a comparison between these cells and the cells of the human liver atlas presented below.

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Human Liver Atlas

Data portal for the paper Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations by MacParland et al. Nat Commun, 2018. This is an RShiny app based on scClustViz for exploring the scRNAseq data presented in the paper.

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Mouse Cerebral Cortex

Data portal for the paper Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling by Yuzwa, Borrett, et al. Cell Rep, 2017. This data portal contains time-series data presented as a set of RShiny apps based on scClustViz.
Timepoints: E11.5 — E13.5 — E15.5 — E17.5