Galaxy |

Seurat UMAP (version 4.0.4+galaxy0)

Choose the format of the input:

Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData

RDS file:

Select RDS file(s) with Seurat object for input

Choose the format of the output:

Seurat, Single Cell Experiment, AnnData or Loom

Dims:

Which dimensions to use as input features, used only if list('features') is NULL

Reduction:

Which dimensional reduction (PCA or ICA) to use for the UMAP input. Default is PCA

Assay:

Assay to pull data for when using list('features') , or assay used to construct Graph if running UMAP on a Graph

N neighbors:

This determines the number of neighboring points used in local approximations of manifold structure. Larger values will result in more global structure being preserved at the loss of detailed local structure. In general this parameter should often be in the range 5 to 50.

N components:

The dimension of the space to embed into.

Local connectivity:

The local connectivity required - i.e. the number of nearest neighbors that should be assumed to be connected at a local level. The higher this value the more connected the manifold becomes locally. In practice this should be not more than the local intrinsic dimension of the manifold.

Seed use:

Set a random seed. By default, sets the seed to 42. Setting NULL will not set a seed

Reduction name:

Name to store dimensional reduction under in the Seurat object

Reduction key:

dimensional reduction key, specifies the string before the number for the dimension names. UMAP by default

Advanced options

Advanced 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.

For more details on this method, please see the individual in-line documentation or the same method's Seurat 4 documentation.

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).