Enhancement: Provide options to set customized cell signatures in Snakemake configuration file

[taoliu]

In the current version 1.0.2, if users use the snakemake pipeline, there is no way to set their customized cell signatures, and they are forced to use CIBERSORT immune cell signatures. The pipeline would be more useful if the cell annotation results from snakemake pipeline can make more sense.

https://github.com/liulab-dfci/MAESTRO/tree/master/MAESTRO/Snakemake

[DongqingSun96]

Hi Tao,

Thanks for this suggestion. In the latest version of MAESTRO, we provide the option to set the custom cell signature through the two arguments both in scRNA and scATAC.

MAESTRO/MAESTRO/Snakemake/scRNA/config.yaml

Lines 16 to 20 in 1fd24fb

	# Flag to provide custom cell signatures [TRUE, FALSE]
	signature: TRUE
	# If signature = TRUE, provide the file location of custom cell signatures.
	# The signature file is tab-seperated. The first column is cell type, and the second column is signature gene.
	signaturefile: /home1/wangchenfei/Project/SingleCell/scATAC/Code/MAESTRO/MAESTRO/annotations/human_immune_CIBERSORT.txt

Thanks!
Dongqing

[taoliu]

Thanks! I will give it a try!