GeneTrajectory
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KlugerLab
R implementation of GeneTrajectory
Hi! Thank you for developing the package!when I download human_myeloid_seurat_obj.rds and run the vignette `data_S$celltype
I don't understand how to determine if a gene is in the end of trajectory, I have a list of markers of interest. they have highers pseudoorder values. ho can...
hi, I have a dataset of integrated KO + WT cells. Is it possible to split in some way the trajectories for each condition in R?
Hi! I installed module gene_trajectory with pip in a conda env.I can comput the gene-gene distances with the seurat data in GeneTrajectory tutorial and the progress _bar are showed in...
I tried to set up a virtualenv using [reticulate], however, I can not find the module. Here is the output: `> cal_ot_mat_from_numpy
After studying the GeneTrajectory tutorial and R script in https://klugerlab.github.io/GeneTrajectory/articles/GeneTrajectory.html and github, I successfully completed the entire process. There are still some confusions that I don’t understand and can’t solve....
I tried to Compute the Diffusion Map cell embedding but there is an error: > pbmc traceback() 4: sequence.default(n..1, from = seq.int(s.1, length(df), s.1), by = size) 3: as.matrix.dist(dist(data.S@reductions[[reduction]]@cell.embeddings[, dims]))...
"When I was working on computing gene-gene distances, I encountered this error. How can I resolve it? Thank you." cal_ot_mat_from_numpy
Hi, I am wondering how to determine/evaluate the ideal N and t.list parameters in the ExtractGeneTrajectory step? For example, in the tutorial, N=3 and t.list = c(4,7,7) were chosen, but...
Hi, I was wondering how to identify the start and end genes in a gene trajectory. It seems genes in some trajectory need to be reversed for biological relevance. Thank...
