Workflow Type: Galaxy
Open
Frozen
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
- Includes Galaxy Workflow Tests
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
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
1.0 (latest) Created 16th Jul 2024 at 14:11 by Helena Rasche
Added/updated 4 files
Open
master
48a5bd4
3.0 (earliest) Created 25th Jun 2024 at 11:16 by Helena Rasche
Added/updated 4 files
Frozen
3.0
4a82b5b
Creators and Submitter
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Activity
Views: 225 Downloads: 95
Created: 25th Jun 2024 at 11:16
Last updated: 25th Jun 2024 at 11:16
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