Clustering 3k PBMC with Scanpy

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Workflow Type: Galaxy

Workflow based on clustering 3K PBMCs with Scanpy tutorial

Associated Tutorial

This workflows is part of the tutorial Clustering 3k PBMC with Scanpy, available in the GTN

Features

Thanks to...

Tutorial Author(s): Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm

Workflow Author(s): Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1259?version=1

Steps

ID Name Description
4 Import Anndata and loom toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.3+galaxy0
5 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
6 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
7 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
8 Filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1
9 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
10 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
11 Select last toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0
12 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
13 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
14 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
15 Concatenate datasets cat1
16 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
17 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
18 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
19 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
20 Filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1
21 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
22 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
23 Filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1
24 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
25 Normalize toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy1
26 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
27 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
28 Filter toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1
29 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
30 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
31 Remove confounders toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy1
32 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
33 Cluster, infer trajectories and embed toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1
34 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
35 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
36 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
37 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
38 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
39 Cluster, infer trajectories and embed toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1
40 Cluster, infer trajectories and embed toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1
41 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
42 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
43 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
44 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
45 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
46 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
47 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
48 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0
49 Inspect and manipulate toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1
50 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
51 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
52 Inspect clusters Here I inspected the louviain clusters... toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
53 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
54 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
55 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
56 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
57 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
58 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
59 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
60 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1
61 Datamash toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0

Version History

2.0 (latest) Created 7th Oct 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master ea3ca25

1.0 Created 16th Jul 2024 at 14:11 by Helena Rasche

Added/updated 4 files


Frozen 1.0 48a5bd4

3.0 (earliest) Created 25th Jun 2024 at 11:16 by Helena Rasche

Added/updated 4 files


Frozen 3.0 4a82b5b
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tool
SCANPY
License
Creative Commons Attribution 4.0 International
Activity

Views: 473   Downloads: 170

Created: 25th Jun 2024 at 11:16

Last updated: 7th Oct 2024 at 14:09

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Total size: 423 KB
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