Clustering 3k PBMCs with Seurat

This is the workflow for the Clustering 3K PBMCs with Seurat tutorial if you are using the separate preprocessing tools (NormalizeData, FindVariableFeatures, ScaleData).

Associated Tutorial

This workflows is part of the tutorial Clustering 3K PBMCs with Seurat, available in the GTN

Features

Thanks to...

Workflow Author(s): Marisa Loach

Tutorial Author(s): Marisa Loach

Tutorial Contributor(s): Pavankumar Videm, Saskia Hiltemann

Inputs

ID	Name	Description	Type
Canonical Markers	Canonical Markers	Paste in a list of canonical markers for PBMCs - this is given in the Clustering 3K PBMCs with Seurat tutorial.	File
barcodes.tsv	barcodes.tsv	Table of barcodes for the cells in the matrix.	File
genes.tsv	genes.tsv	Table of gene names for the features in the matrix.	File
matrix.mtx	matrix.mtx	Single cell expression data in Matrix Market (mtx) format. This is the table that shows the counts of each RNA in each cell.	File

Steps

ID	Name	Description
4	Input 3k PBMC	toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1
5	Seurat Data Management	toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0
6	Mitochondrial Annotations	toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1
7	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
8	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
9	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
10	Filtered Dataset	toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1
11	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
12	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
13	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
14	Seurat Preprocessing	toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0
15	Seurat Preprocessing	toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0
16	Preprocessed Data	toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0
17	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
18	PCA Results	toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0
19	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
20	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
21	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
22	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
23	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
24	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
25	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
26	Seurat Find Clusters	toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0
27	Seurat Find Clusters	toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0
28	UMAP Results	toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0
29	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
30	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
31	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
32	DE Markers	toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0
33	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
34	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
35	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
36	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
37	Annotated Clusters	This is the final annotated Seurat Object with each cluster labelled by cell type. toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0
38	DE Markers (Tabular)	csv_to_tabular
39	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
40	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0
41	Input DE Markers	Cut1
42	Seurat Visualize	toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0

Outputs

ID	Name	Description	Type
Input 3k PBMC	Input 3k PBMC	n/a	File
Preprocessed Data	Preprocessed Data	n/a	File
Annotated Clusters	Annotated Clusters	n/a	File
Input DE Markers	Input DE Markers	n/a	File

Clustering 3k PBMCs with Seurat - Workflow
1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 27th Jan 2025 at 13:07 by Helena Rasche

Creators

Submitter

Clustering 3k PBMCs with Seurat - Workflow 1.0

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (earliest) Created 27th Jan 2025 at 13:07 by Helena Rasche

Creators

Submitter

Related items

Clustering 3k PBMCs with Seurat - Workflow
1.0