AnnData object to Monocle input files

Preparing and filtering gene and cell annotations files and expression matrix to be passed as input for Monocle

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

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	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 unwanted cell types	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

Outputs

ID	Name	Description	Type
Cells without macrophages	#main/Cells without macrophages	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
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
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
Unprocessed expression matrix	#main/Unprocessed expression matrix	n/a	File
filtered matrix (by cells) transposed	#main/filtered matrix (by cells) transposed	n/a	File