Trajectory analysis using Monocle3 - full tutorial workflow
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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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1228?version=1

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 25th Jun 2024 at 11:13 by Helena Rasche

Added/updated 4 files


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Views: 473   Downloads: 103

Created: 25th Jun 2024 at 11:13

Last updated: 25th Jun 2024 at 11:13

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