Seurat.Clustering

LSID

urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00408

Author(s)

Satija Lab, NY Genome Center, wrapped as a module by Ted Liefeld, Mesirov Lab, UCSD School of Medicine.

Contact(s)

Algorithm and scientific questions: satijalab.org

Module wrapping issues:  Ted Liefeld  < jliefeld at cloud dot ucsd dot edu>

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Introduction

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

Within GenePattern, Seurat is accessed as several different modules exposing different portions of the Seurat workflow; Seurat.Preprocessing, Seurat.BatchCorrection, Seurat.QC and Seurat.Clustering. This module, Seurat.Clustering performs UMAP clustering and marker identification on single-cell RNA-Seq data.

Algorithm

The Seurat.Clustering module performs uses Seurat version 3.0.2. It performs following steps from Seurat to the input dataset;

1. FindNeighbors
2. FindClusters
3. RunUMAP
4. DimPlot

For details of the Seurat implementation please refer to the Seurat documentation from the Satija lab.

References

https://satijalab.org/seurat/

Input Files

1. input seurat rds file*
   A RDS (from the R programming language) file containing a Seurat object.

Output Files

1. <output filename>.rds
   Output RDS file containing a Seurat object that contains the cluster details for optional further processing.
2. <output filename>_all_markers.csv
   Comma delimited file containing "p_val","avg_logFC","pct.1","pct.2","p_val_adj","cluster","gene" for the marker genes.
3. <output_filename>.clustered.csv
   Comma delimited file containing "p_val","avg_logFC","pct.1","pct.2","p_val_adj","cluster","gene" for the identified gene clusters.
4. <output_filename>.clustered.pdf
   PDF formatted file containing the UMAP plot of the clusters.

Example Data

mat_notRegressed.rds

Requirements

GenePattern 3.9.11 or later (dockerized).

Parameters

Name	Description
input seurat rds file*	A rds file containig a Seurat object.
output filename*	The output filename prefix used for all output files.
maximum dimension	The maximum number of clusters to attempt to find.
resolution*	The resolution to use to find clusters.
reduction*	The reduction to use (UMAP). Other reductions (e.g. TSNE) may be added later.
seed*	The random number seed to use.

* - required