In nasqar/SeuratWizard: User Interface to Seurat (Single Cell) in R Shiny

Introduction

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This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

The wizard style makes it intuitive to go back between steps and adjust parameters based on different outputs/plots, giving the user the ability to use feedback in order to guide the analysis iteratively.

It is meant to provide an intuitive interface for researchers to easily upload, analyze, visualize, and explore single-cell RNA-seq data interactively with no prior programming knowledge in R.

It is based on Seurat, an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

The application follows the Seurat - Guided Clustering Tutorial workflow closely. It also provides additional functionalities to further explore and visualize the data.

See Figure 1 below for a diagram that outlines all the workflow steps and their expected output

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Figure 1: Workflow (Click figure to enlarge)

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Input Data Types

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This application accepts the following types of input data:

1. Example data (Demo):

• For demo purposes, you can select "Example data"

• That will automatically load the PBMC data used in the tutorial

• You can follow the steps afterwards to run the analysis mirroring the tutorial in order to get familiar with the app

2. Upload your own data (gene counts):

• A .csv/.txt file that contains a table of the gene counts

• The first column should have gene names/ids followed by columns for sample counts. The file can be either comma or tab delimited

• If your counts are not merged, you can use this Count Merger to consolidate all your sample count files

• Make sure cell/column names do NOT contain underscores _ unless they are replicates

• For replicates, denote column names with underscore plus the replicate number (eg. Sample_1)

• First column can either contain gene.ids or gene.names

• For a sample file, click here

Figure 2: Eg. counts file

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2. 10X data

• This option requires uploading 3 files: 1 .mtx file, and 2 .tsv files

• See the example in the tutorial, or click here to download the PBMC data.

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Run Results

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1. Data Output

There will be plenty of output information from major steps, some of which will be displayed and/or downloadable - Genes in PCs - List of cells in each cluster - List of differentially expressed genes - Seurat Object (.RObj) containing all steps and computed data output

2. Visualization

Various forms of visualizations are included: QC/Filter * Violin Plot * Gene Plot * Dispersion Plot Dimensionality Reduction * PCA Plot * Heatmap Clustering * Jackstraw / Elbow Plots * tSNE Plot Gene Expression * Violin Plot * Feature Plot

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nasqar/SeuratWizard documentation built on Sept. 24, 2019, 2:02 p.m.