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MAGIC adaptive kernel #106
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Hi David thanks for getting in touch! After reading the paper I was keen to try it out, so coded up that simple implementation. As you rightly point out, it's missing the adaptive kernel. This R implementation is not "release ready", so I have not exported the MAGIC functions in the latest devel versions of the pkg (i.e. not visible to the user), which will be released in the next Bioconductor release. (I'd also been meaning to get in touch with you, but things got away from me.) It would be great to have your advice on correctly implementing MAGIC. I think it would be excellent to have an R version available to people, and should enable more people to use your method. Best |
Hi Davis, Here's a Matlab implementation of MAGIC that doesn't require an external diffusion map package: %% params %% MAGIC %% rescale stuff here (you already have that) Above code should be fairly easily ported to R. David |
Pretty cool, it'd be great to have the R equivalent of this implementation available in scater. |
When I have time I'll try to implement this in R. I'll post it here when I do. |
This issue was moved to alanocallaghan/scater#21 |
I saw that there is a MAGIC implementation in Scater, however it doesn't use the adaptive kernel. The adaptive kernel is important for MAGIC to work well. I haven't coded in R for a long time but I can advise on how to correctly implement MAGIC.
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