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Seurat FindMarkers (version 4.0.4+galaxy0)
Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData
Select RDS file(s) with Seurat object for input
A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs).
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals.
Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf).
Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests.
Advanced Options
Advanced Options 0

What it does

This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset. It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)

p-value adjustment is performed using bonferroni correction based on the total number of genes in the dataset. Other correction methods are not recommended, as Seurat pre-filters genes using the arguments above, reducing the number of tests performed. Lastly, as Aaron Lun has pointed out, p-values should be interpreted cautiously, as the genes used for clustering are the same genes tested for differential expression.

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.

Inputs

  • RDS object

Outputs

  • Text file

Version history 4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.

3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.

3.1.2_0.0.8: Update metadata parsing

3.1.1_0.0.7: Exposes perplexity and enables tab input.

3.1.1_0.0.6+galaxy0: Moved to Seurat 3.

Find clusters: removed dims-use, k-param, prune-snn.

2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).

0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).