Some questions about the input data for scMTNI

[jingkun12137]

My data was on scRNA-seq and scATAC-seq on a group of mouse ILC cells. Following Shilu Zhang's method on github, I used liger to get the clustering results of the cells, but there were some issues that prevented me from proceeding.

1. I'm not sure how ExampleData/cluster*.table is obtained

2. Should cluster_allGenes.txt and cluster_allregulators manually input some interested gene and regulators, or is there any way to get them quickly

3. What I am interested in is only the influence of regulators on genes in ILC cells. Do I still need to construct a cell lineage tree

[SuvojitHazra]

Hello Jingkun Yi,

Thank you for your interest in scMTNI.

(1) As you asked, I would like to answer your third question first. scMTNI is a multi-task learning GRN (gene regulatory network) inference approach that always takes cell-lineage tree, scRNA-seq expression and/or scATAC-seq data as inputs to infer GRN for each cell-type on a cell-lineage. Therefore, you always need to construct a cell-lineage as you already have scRNA-seq expression and scATAC-seq data on a group of mouse ILC cells.

(2) Now coming to your first query, you have to make a data folder 'ExampleData' in your working directory, then, you have to put cell-type specific table files i.e., cluster.table. Frankly speaking, you do not have to exactly follow the naming of these files, however, following the standard is always best. Otherwise, you can make text files like cluster.txt or celltype*_expression.txt etc. inside the 'ExampleData' folder where, you have the matrix (gene x cell) information of scRNA-seq data for each cell cluster/celltype from you cell lineage tree. See https://github.com/Roy-lab/scMTNI for more details.

(3) For your second query, no shortcut or quick cheat code is there to generate cell-type/cluster specific cluster_allGenes.txt and cluster_allregulators.txt files. You specifically have to follow the step regarding running of the script namely, 'PreparescMTNIinputfiles.py' of https://github.com/Roy-lab/scMTNI tutorial.

Kindly write us if you have any more queries.

Cheers, Suvojit.

Please cite this if you use scMTNI: Zhang, S., Pyne, S., Pietrzak, S., Halberg, S., McCalla, S.G., Siahpirani, A.F., Sridharan, R. and Roy, S., Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 14, 3064 (2023). https://doi.org/10.1038/s41467-023-38637-9