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rna-qc-tool

A Shiny app for interactive visualization of sinlge-cell RNA quality control statistics.

How it works?

Click on Browse button in the left pane and upload a (.h5) file. Specify the input parameters (or leave default values). After uploading is complete, click Apply Filter button. The application automatically annotates mitochondrial and ribosomal genes. Next, it filters all the cells and features based on parameters selected in the left pane, in real-time. There parameters can be adjusted anytime.

In a few seconds, 2 tabs on the right will be populated:

  • Table: lists all the commonly used statistics for filtered dataset

  • Plots: generates all commonly used figures to visualize filtered dataset

Features

  1. The plots are rendered live (changing parameters will change both tabs live)

  2. The plots are interactive (hover mouse over plots to zoom, see specific values)

  3. Download Script button allows you to download scripts that are pre-populated with selected parameters for quality control in Python (using scanpy) and R (seurat)