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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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How to compute the variance of genes using 'gam'. #58

Closed mahp-scut closed 2 years ago

mahp-scut commented 2 years ago

Hi, Thank you very much for this tool. I am preprocessing other scRNA-seq dataset following the procedure mentioned in your paper, that is, "We used the general additive model implemented in the ‘gam’ R package to compute the variance and the P value of this variance". However, i don't know how to compute the variance of genes using the ‘gam’ R package. It will be great if you can provide some example codes! Thanks!

adyprat commented 2 years ago

The R notebooks for pre-processing experimental scRNA-seq datasets are now under https://github.com/Murali-group/Beeline/tree/master/inputs/scRNAseq_preprocessing. The data sources (for input files) are listed in the notebooks.

mahp-scut commented 2 years ago

Thank you very much for your response!