Workflow Type: Galaxy
Open
Trajectory analysis using Monocle3, starting from AnnData
Associated Tutorial
This workflows is part of the tutorial Trajectory analysis using Monocle3 - full tutorial workflow, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Julia Jakiela
Tutorial Contributor(s): Helena Rasche, Wendi Bacon
Workflow Author(s): Julia Jakiela
Funder(s): EPSRC Training Grant DTP 2020-2021 Open University
Inputs
ID | Name | Description | Type |
---|---|---|---|
AnnData before processing to extract clean expression matrix | #main/AnnData before processing to extract clean expression matrix | n/a |
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AnnData to extract genes & cells annotations | #main/AnnData to extract genes & cells annotations | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | Extract cell annotations | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
3 | Extract gene annotations | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
4 | Extract clean expression matrix | Unprocessed means here before normalisation or dimensionality reduction. For this step, must have cell IDs as rownames. toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
5 | Filter out macrophages | Double-check the cell_type column number Filter1 |
6 | gene_short_name annotation | Check the number of the column with genes names (using column) and its header (Find Regex) toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2 |
7 | Cut cells IDs | Cut1 |
8 | Cut genes IDs | Cut1 |
9 | Filter matrix (by cells) | join1 |
10 | Remove duplicate column (cells IDs) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
11 | Transpose matrix | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2 |
12 | Filter matrix (by genes) | join1 |
13 | Remove duplicate column (genes IDs) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
14 | Monocle3 create | Check the data format that you're using. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 |
15 | Monocle3 preprocess | You might want to change the dimensionality of the reduced space here. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0 |
16 | Monocle3 reduceDim | UMAP/tSNE/PCA/LSI. However for further steps you need to use UMAP. toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0 |
17 | Monocle3 partition | You might want to change resolution (affects clusters) and/or q-value (affects partitions). toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0 |
18 | Plot cell type | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
19 | Plot genotype | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
20 | Plot batch | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
21 | Plot sex | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
22 | Monocle3 top markers | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0 |
23 | Plot genes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
24 | Plot partition | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
25 | Plot cluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
26 | Monocle3 learnGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0 |
27 | Plot learned trajectory | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
28 | Monocle3 orderCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0 |
29 | Monocle3 diffExp | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1 |
30 | Plot pseudotime | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Batch plot | #main/Batch plot | n/a |
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Cell type plot | #main/Cell type plot | n/a |
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Cell types & learned trajectory path plot | #main/Cell types & learned trajectory path plot | n/a |
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Cells without macrophages | #main/Cells without macrophages | n/a |
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Cluster plot | #main/Cluster plot | n/a |
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Differential expression of genes - table | #main/Differential expression of genes - table | n/a |
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Extracted cell annotations (obs) | #main/Extracted cell annotations (obs) | n/a |
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Extracted gene annotations (var) | #main/Extracted gene annotations (var) | n/a |
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Filtered cells IDs | #main/Filtered cells IDs | n/a |
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Filtered matrix (by cells & genes) | #main/Filtered matrix (by cells & genes) | n/a |
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Filtered matrix (by cells) | #main/Filtered matrix (by cells) | n/a |
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Gene expression plot | #main/Gene expression plot | n/a |
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Genes IDs | #main/Genes IDs | n/a |
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Genes table with gene_short_name colname | #main/Genes table with gene_short_name colname | n/a |
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Genotype plot | #main/Genotype plot | n/a |
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Monocle3 create on input dataset(s): cds3 | #main/Monocle3 create on input dataset(s): cds3 | n/a |
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Monocle3 learnGraph on input dataset(s): cds3 | #main/Monocle3 learnGraph on input dataset(s): cds3 | n/a |
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Monocle3 orderCells on input dataset(s): cds3 | #main/Monocle3 orderCells on input dataset(s): cds3 | n/a |
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Monocle3 partition on input dataset(s): cds3 | #main/Monocle3 partition on input dataset(s): cds3 | n/a |
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Monocle3 preprocess on input dataset(s): cds3 | #main/Monocle3 preprocess on input dataset(s): cds3 | n/a |
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Monocle3 reduceDim on input dataset(s): cds3 | #main/Monocle3 reduceDim on input dataset(s): cds3 | n/a |
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Partition plot | #main/Partition plot | n/a |
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Pre-filtered matrix (by cells & genes) | #main/Pre-filtered matrix (by cells & genes) | n/a |
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Pre-filtered matrix (by cells) | #main/Pre-filtered matrix (by cells) | n/a |
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Pseudotime plot | #main/Pseudotime plot | n/a |
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Sex plot | #main/Sex plot | n/a |
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Unprocessed expression matrix | #main/Unprocessed expression matrix | n/a |
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_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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filtered matrix (by cells) transposed | #main/filtered matrix (by cells) transposed | n/a |
|
Version History
1.0 (earliest) Created 25th Jun 2024 at 11:13 by Helena Rasche
Added/updated 4 files
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Created: 25th Jun 2024 at 11:13
Last updated: 25th Jun 2024 at 11:13
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