Mahmoud A. Bassal

Hi @andrea-de-micheli, I had issues with the same function when importing SPRING coordinates. What I realized was the coordinates needed to be within the scale of at most 10-20. Turns...

Id just try going smaller still maybe even divide the coordinates by 10 and see how it goes. For me I just kept going smaller and smaller till it eventually...

Having the same issue and would appreciate any help. @pkharchenko, happy to share the data confidentially to help you track down what the issue could be. Im trying to get...

traceback() ```R 4: stop("'from' must be a finite number") 3: seq.default(rx[1], rx[2], length.out = grid.n) 2: seq(rx[1], rx[2], length.out = grid.n) 1: show.velocity.on.embedding.cor(emb_matrix, rvel.cd, n = 200, scale = "sqrt",...

@pkharchenko, any updates regarding this?

Hi @VPetukhov, Has there been any developments on this? What do you recommend as the best way to deal with v3 indrop fq files?

Hi I guess to the same spirit as the previous question. So in the documentation you outline the structure of R1 with the UMI position and then R2 with the...

I have fq for the ab's and for the hto's seperate to the expression data (ie the fq have been split into the different samples, and each sample has its...

Similar problem when attempting to build annotations ``` build_annotations(genome = 'mm10', annotations = "mm10_cpgs") ``` I then get back the error ``` Building CpG islands... Error in open.connection(5L, "rb") :...

Ok so it seems in the build_annotation.R file, the following URL ``` http://hgdownload.cse.ucsc.edu/ ``` needs to be changed to ``` http://hgdownload2.cse.ucsc.edu/ ``` So, change the lines in question (5 in...