Trajectory analysis using Monocle3 - full tutorial workflow 1.0
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Workflow Type: Galaxy
Trajectory analysis using Monocle3, starting from AnnData
Associated Tutorial
This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Julia Jakiela
Tutorial Author(s): Julia Jakiela
Tutorial Contributor(s): Helena Rasche, Wendi Bacon, Pavankumar Videm, Julia Jakiela, Saskia Hiltemann, Mehmet Tekman, Matthias Bernt, Pablo Moreno, Björn Grüning
Grants(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 |
|
| 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 |
|
| Cell type plot | #main/Cell type plot | n/a |
|
| Cell types & learned trajectory path plot | #main/Cell types & learned trajectory path plot | n/a |
|
| Cells without macrophages | #main/Cells without macrophages | n/a |
|
| Cluster plot | #main/Cluster plot | n/a |
|
| Differential expression of genes - table | #main/Differential expression of genes - table | n/a |
|
| Extracted cell annotations (obs) | #main/Extracted cell annotations (obs) | n/a |
|
| Extracted gene annotations (var) | #main/Extracted gene annotations (var) | n/a |
|
| Filtered cells IDs | #main/Filtered cells IDs | n/a |
|
| Filtered matrix (by cells & genes) | #main/Filtered matrix (by cells & genes) | n/a |
|
| Filtered matrix (by cells) | #main/Filtered matrix (by cells) | n/a |
|
| Gene expression plot | #main/Gene expression plot | n/a |
|
| Genes IDs | #main/Genes IDs | n/a |
|
| Genes table with gene_short_name colname | #main/Genes table with gene_short_name colname | n/a |
|
| Genotype plot | #main/Genotype plot | n/a |
|
| Monocle3 create on input dataset(s): cds3 | #main/Monocle3 create on input dataset(s): cds3 | n/a |
|
| Monocle3 learnGraph on input dataset(s): cds3 | #main/Monocle3 learnGraph on input dataset(s): cds3 | n/a |
|
| Monocle3 orderCells on input dataset(s): cds3 | #main/Monocle3 orderCells on input dataset(s): cds3 | n/a |
|
| Monocle3 partition on input dataset(s): cds3 | #main/Monocle3 partition on input dataset(s): cds3 | n/a |
|
| Monocle3 preprocess on input dataset(s): cds3 | #main/Monocle3 preprocess on input dataset(s): cds3 | n/a |
|
| Monocle3 reduceDim on input dataset(s): cds3 | #main/Monocle3 reduceDim on input dataset(s): cds3 | n/a |
|
| Partition plot | #main/Partition plot | n/a |
|
| Pre-filtered matrix (by cells & genes) | #main/Pre-filtered matrix (by cells & genes) | n/a |
|
| Pre-filtered matrix (by cells) | #main/Pre-filtered matrix (by cells) | n/a |
|
| Pseudotime plot | #main/Pseudotime plot | n/a |
|
| Sex plot | #main/Sex plot | n/a |
|
| Unprocessed expression matrix | #main/Unprocessed expression matrix | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| filtered matrix (by cells) transposed | #main/filtered matrix (by cells) transposed | n/a |
|
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Views: 1379 Downloads: 167 Runs: 0
Created: 2nd Jun 2025 at 10:57
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