Galaxy |

Seurat (version 4.3.0.1+galaxy1)

Which Seurat method should be run?:

Counts file:

The should be a TAB-separated count matrix with gene identifers in the first column and a header row

Minimum cells:

Include genes with detected expression in at least this many cells

Minimum genes:

Include cells where at least this many genes are detected

Low threshold for filtering cells:

High threshold for filtering cells:

Include violin plot and scatter plot of cell features:

Output seurat object after data normalization:

Continue workflow after Normalization step?:

Output options

Output options 0

What it does

Seurat is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. It is developed and maintained by the Satija Lab at NYGC. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See the Seurat Guided Clustering tutorial for more information.

Inputs

Gene count matrix in TAB-separated format

or

RNA and Protein count matrices in TAB-separated formats

Outputs

HTML of plots

Optionally you can choose to output

R commands used to generate plots printed alongside figures