scanpy-clustering/main
v0.1

Workflow Type: Galaxy

Single-cell RNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. It takes count matrix, barcodes and feature files as input and creates an Anndata object out of them. It then performs QC and filters for lowly expressed genes and cells. Then the data is normalized and scaled. Then PCs are computed to further cluster using louvain algorithm. It also generated various plots of clustering colored with highly ranked genes.

SEEK ID: https://workflowhub.eu/workflows/1256?version=1

Inputs

ID	Name	Description	Type
Annotate louvain clusters with these cell types	Annotate louvain clusters with these cell types	Provide a comma-separated list of cell types to annotate the louvain clusters.	string?
Barcodes	Barcodes	A cell barcodes file with a single barcode in each line. The barcodes should correspond to the cells in the matrix file	File
Genes	Genes	A genes/features tabular file with gene ids and gene symbols	File
Input is from Cell Ranger v2 or earlier versions	Input is from Cell Ranger v2 or earlier versions	v2 genes.tsv file contains two columns with Gene ID and Gene Name. v3 features.tsv file contains three columns Feature ID, Feature Name, Feature Type	boolean
Louvain resolution	Louvain resolution	Louvain clustering resolution. Higher resolution means finding more and smaller clusters. If not set, a default value of 1.0 is used.	float?
Manually annotate celltypes?	Manually annotate celltypes?	You must have run the workflow at least once, to know the number of clusters and the cell types inferred.	boolean
Matrix	Matrix	A single-cell count matrix file in Matrix Market Exchange format	File
Maximum number of genes expressed	Maximum number of genes expressed	Maximum number of genes expressed per cell. If not set, a default of 2500 is used.	int?
Minimum number of cells expressed	Minimum number of cells expressed	use a small number. Generally 3-5. If not set, a default of 3 is used.	int?
Minimum number of genes expressed	Minimum number of genes expressed	Minimum number of genes expressed per cell. If not set, a default of 200 is used.	int?
Mitochondrial genes start with pattern	Mitochondrial genes start with pattern	For eg MT- or M-	string?
Number of PCs to use for computing neighborhood graph	Number of PCs to use for computing neighborhood graph	This parameter can be estimated from an Elbow plot of PC loadings.	int?
Number of neighbours for computing neighborhood graph	Number of neighbours for computing neighborhood graph	Size of the local neighborhood. If not set a default of 15 is used.	int?

Steps

ID	Name	Description
13	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
14	Anndata from 10x v2 or earlier	toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0
15	Map and switch the input CellRager version	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
16	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
17	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
18	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
19	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
20	Anndata from 10x V3 or later	toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0
21	Choose the Anndata	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
22	Filter genes by cells expressed	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0
23	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0
24	Flag Mitochondrial genes	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0
25	Calculate quality metrics	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
26	Scatter plot n_genes vs pct_mito	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
27	Scatter plot n_counts vs n_genes	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
28	Violin plot n_genes, n_counts, pct_mito	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
29	Filter cells by min genes expressed	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0
30	Filter cells by max genes expressed	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0
31	Filter cells by percentage of mito genes	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0
32	Normalize by target sum	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0
33	Logarithmize	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
34	Freeze raw attribute	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0
35	Annotate highly variable genes	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0
36	Manipulate AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0
37	Plot highly variable	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
38	Regress out	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0
39	Scale data	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
40	Compute PCA	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0
41	Compute Neighborhood graph	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
42	Scanpy plot	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
43	Scanpy plot	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
44	Scanpy plot	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
45	Embed using UMAP	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0
46	Louvain clustering	Higher resolution means finding more and smaller clusters. toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0
47	UMAP of louvain	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
48	Rank genes by Wilcoxon test	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1
49	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0
50	Inspect clusters	Here I inspected the louviain clusters... toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0
51	Scanpy plot	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
52	Manipulate AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0
53	General information about the final Anndata object	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0
54	Select top ranked genes	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
55	Count number of clusters	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
56	Select top ranked genes with louvain	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
57	Count number of cells per cluster	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
58	Pick parameter value	toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0
59	Parse parameter value	param_value_from_file
60	Parse parameter value	param_value_from_file
61	Parse parameter value	param_value_from_file
62	Scanpy plot	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
63	Violin plot of top genes on clusters	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
64	Stacked violin of top genes on clusters	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
65	Dotplot of top genes on clusters	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
66	Heatmap of 20 genes	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0
67	UMAP of louvain and top ranked genes	toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0

Outputs

Version History

v0.1 (earliest) Created 26th Jan 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 e0bd0d5

Creators and Submitter

Creators

Pavankumar Videm
Hans-Rudolf Hotz
Mehmet Tekman
Bérénice Batut

Submitter

WorkflowHub Bot

Tools

anndata

SCANPY

License

Creative Commons Attribution 4.0 International

Activity

Views: 29 Downloads: 4 Runs: 0

Created: 26th Jan 2025 at 03:01

ID	Name	Description	Type
Initial Anndata General Info	Initial Anndata General Info	n/a	File
Scatter plot of n_genes vs pct_mito	Scatter plot of n_genes vs pct_mito	n/a	File
Scatter plot of plot n_counts vs n_genes	Scatter plot of plot n_counts vs n_genes	n/a	File
Violin plot n_genes, n_counts, pct_mito	Violin plot n_genes, n_counts, pct_mito	n/a	File
Anndata with raw attribute	Anndata with raw attribute	n/a	File
Plot highly variable	Plot highly variable	n/a	File
Plot genes according to contributions to PCs	Plot genes according to contributions to PCs	n/a	File
Plot PCA over view with genes	Plot PCA over view with genes	n/a	File
Elbow plot of PCs and variance	Elbow plot of PCs and variance	n/a	File
UMAP of louvain	UMAP of louvain	n/a	File
Ranked genes with Wilcoxon test	Ranked genes with Wilcoxon test	n/a	File
Plot Rank gene groups	Plot Rank gene groups	n/a	File
Anndata with Celltype Annotation	Anndata with Celltype Annotation	n/a	File
General information about the final Anndata object	General information about the final Anndata object	n/a	File
Number of cells per cluster	Number of cells per cluster	n/a	File
UMAP with annotated cell types	UMAP with annotated cell types	n/a	File
Violin plot of top genes on clusters	Violin plot of top genes on clusters	n/a	File
Stacked violin of top genes on clusters	Stacked violin of top genes on clusters	n/a	File
Dotplot of top genes on clusters	Dotplot of top genes on clusters	n/a	File
Heatmap of top 20 highly ranked genes	Heatmap of top 20 highly ranked genes	n/a	File
UMAP of louvain and top ranked genes	UMAP of louvain and top ranked genes	n/a	File

scanpy-clustering/main v0.1