SingleCellTable
Authors: Matilde Sanches, Maite Saura Sanchez
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Full Description:
What?
scTable is an interactive website for visualizing tables generated from scRNA-seq data with the functions FindMarkers() or FindAllMarkers() of Seurat in an intuitive way without coding knowledge.
Why?
scRNA-seq technologies are becoming more and more popular. Therefore a huge amount of single cell data is becoming available for the scientific community to use for generating work hypothesis. However, the analysis of the data in R requires coding knowledge and it may be not accessible for wet lab scientists.
To overcome this limitation, a table of marker genes that are induced in the clusters of a single cell experiments is often share as a supplemental data. This table allows to the users to look for genes of interest. However, this is often done in a very basic way using Microsoft Excel and it requires to check afterwards the global expression of a gene of interest using another visualization tool.
To help wet lab scientist to be able to work with this data, we have generated an application in R that requires only two text files and allows to the user:
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Visualize the list of markers of a single cell experiment.
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Easily visualize the pattern of a certain gene thanks to an abstract representation of the data in a plot within the table. Every square of the plot represents a cluster. If a certain gene is marker of a certain cluster, an inside circle will appear. The diameter of the circle represents the percentage of cells expressing the marker within the cluster (pct.1) and the gradient color the level of gene expression (avg_log2FC).
How?
scTable is prepared to process files generated with the package Seurat. Two files are needed:
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A text file with the markers of the clusters generated with
FindAllMarkers()orFindMarkers()functions. scTable only supports markers with avg_log2FC > 0. -
A text file with the UMAP coordinates of every cell and the cluster annotation, matching the clusters in the markers file.
The files can be submitted to the shiny app and the table will be automatically generated.
Other comments
This table is a prototype of an idea. Due to time constrains, we have uploaded a preliminary version to be able to participate in the Table Contest 2024. We aim to update the application for being more useful, efficient and better documented.
Table Type: interactive-Shiny
Submission Type: Single Table Example
Table: SingleCellTable
Code: GitHub - teima90/SingleCellTable: Code for reproducing SingleCellTable submission to Table contest 2024
Language: R
Industries: Life science, Bioinformatics.
Packages: DT, shiny, reactable, tidyverse, shinydashboard, sparkline,ggforce,ggnewscale,scales