Trajectory analysis using Monocle3 - full tutorial workflow
1.0

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

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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
AnnData before processing to extract clean expression matrix #main/AnnData before processing to extract clean expression matrix n/a
  • File
AnnData to extract genes & cells annotations #main/AnnData to extract genes & cells annotations n/a
  • File

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
  • File
Cell type plot #main/Cell type plot n/a
  • File
Cell types & learned trajectory path plot #main/Cell types & learned trajectory path plot n/a
  • File
Cells without macrophages #main/Cells without macrophages n/a
  • File
Cluster plot #main/Cluster plot n/a
  • File
Differential expression of genes - table #main/Differential expression of genes - table n/a
  • File
Extracted cell annotations (obs) #main/Extracted cell annotations (obs) n/a
  • File
Extracted gene annotations (var) #main/Extracted gene annotations (var) n/a
  • File
Filtered cells IDs #main/Filtered cells IDs n/a
  • File
Filtered matrix (by cells & genes) #main/Filtered matrix (by cells & genes) n/a
  • File
Filtered matrix (by cells) #main/Filtered matrix (by cells) n/a
  • File
Gene expression plot #main/Gene expression plot n/a
  • File
Genes IDs #main/Genes IDs n/a
  • File
Genes table with gene_short_name colname #main/Genes table with gene_short_name colname n/a
  • File
Genotype plot #main/Genotype plot n/a
  • File
Monocle3 create on input dataset(s): cds3 #main/Monocle3 create on input dataset(s): cds3 n/a
  • File
Monocle3 learnGraph on input dataset(s): cds3 #main/Monocle3 learnGraph on input dataset(s): cds3 n/a
  • File
Monocle3 orderCells on input dataset(s): cds3 #main/Monocle3 orderCells on input dataset(s): cds3 n/a
  • File
Monocle3 partition on input dataset(s): cds3 #main/Monocle3 partition on input dataset(s): cds3 n/a
  • File
Monocle3 preprocess on input dataset(s): cds3 #main/Monocle3 preprocess on input dataset(s): cds3 n/a
  • File
Monocle3 reduceDim on input dataset(s): cds3 #main/Monocle3 reduceDim on input dataset(s): cds3 n/a
  • File
Partition plot #main/Partition plot n/a
  • File
Pre-filtered matrix (by cells & genes) #main/Pre-filtered matrix (by cells & genes) n/a
  • File
Pre-filtered matrix (by cells) #main/Pre-filtered matrix (by cells) n/a
  • File
Pseudotime plot #main/Pseudotime plot n/a
  • File
Sex plot #main/Sex plot n/a
  • File
Unprocessed expression matrix #main/Unprocessed expression matrix n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
filtered matrix (by cells) transposed #main/filtered matrix (by cells) transposed n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:57 by GTN Bot

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Created: 2nd Jun 2025 at 10:57

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