hwick
hwick
I have added a note to the lesson to remind people to read the output messages which state where the pathview image has been saved
I am also having this issue. I set categorySize to pvalue, but the legend shows "size" instead of p value and there is no difference to graphs where I do...
update: Not only is nperm deprecated, but it also appears that there are kind of two versions of gse: fgsea and fgseaMultilevel: ``` > gseaKEGG
The default FDR cutoff in degCovariates is 0.1 and all of the non-NA FDR values shown here are significant by that cutoff. DegCovariates says it will highlight and shade significant...
Thank you for looking into this. I will have to check about sending an Robject later as I am not working on this data at the moment, but I can...
Niubile001, can you clarify how to install it from the link you provided? Is there a way to do this from R? If not, what is to be done with...
I was able to install it with `remotes::install_github('satijalab/azimuth', ref = 'v0.4.4')` neither 4.6 nor 4.5 appear to be compatible with seurat v4
As of 3.5.24, code still doesn't work, even with updated sratoolkit. One possible useful addition to this lesson could be to use curl after looking up the individual SRAs https://sra-explorer.info/#training-admin
I've updated the links to the internet archive and noted in the lesson that it's no longer maintained. The only reason I am not closing this issue yet is because...
I noticed FA is part of the on-going DGE discussion, so maybe we can take ideas from the upcoming core meetings about that, too