ilyakorsunsky
ilyakorsunsky
Sure! I cropped a sample of my image and saved it as a tiff with tifffile in python. I cropped a blank region since the full image contains unpublished data....
Thanks @kadyb! That is the work around I'm using for now. In the future, I would really like to use stars for this, since some of my images are too...
Dear @Emma-1991, From the error message, it sounds like there may be an issue with the dimension of the matrix passed to DDRTree. Have you tried to transpose it first?...
Dear @L1H0n9Jun and @yingyonghui, That's right, we removed this support during one of the pushes. Please let me know if you still need to run harmony with Seurat v2 and...
Dear @nshedd and @cswoboda, This is an active problem that we are pursuing and hope to have something out in the next version of Harmony. If you're interested, please let...
Dear @Vivianstats, @rschauner, and @paupaiz, If you are still having issues installing harmony with devtools, please try to install it through CRAN with `install.packages("harmony")`. Please let me know if this...
Dear @favilaco, thanks for offering this solution!
Dear all, Harmony is now available on CRAN! Please try to install through `install.packages("harmony")`. I hope this makes the process more painless and you can get back to your analyses...
Hi Jack, Thanks for the question! With such a large matrix, I would recommend two things: (1) Subset to highly variable genes. (2) Use a memory efficient PCA package and...