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wondering how to generate this file for use with the genes_correlated_with_pseudotime.py script
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Hi,
I have two distinct branches in my UMAP and I want to graph the expression of two genes (each of which mark one branch) on the same pseudotime expression graph. This was capable using Monocle2,…
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Hi,
Is there a reason that almost all genes I plotted had spiky trend curve instead of smooth curves?
Is there a solution to it? Thanks so much!
Regards,
Wen
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Hi,
I'd like to know what should I set for num_cluster. In the documentation, it says "number of clusters for the heatmap of branch genes". Is this the number of clusters I want to have with my d…
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@rcannood @Xiaojieqiu Hello,thank you for your work.
First ,I have to say tha I have compared the both methods to do pseodotime analysis.One is by importing Seurat batch corrected integrated data to …
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Hi Dr. Hou!
I encountered the following choleski error when running `lamian_test()`: suspect it's a dataset-dependent issue, but wanted to reach out to see if you have any thoughts on troubleshooti…
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Hi,
I am trying to add an annotation column on the plot_pseudotime_heatmap function in order to link each plot column to a cluster or state. However I get this error:
Error in plot_pseudotime_h…
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plot_genes_in_pseudotime(AFD_lineage_cds,
color_cells_by="pseudotime",
min_expr=0.5)
Anybody having this error?
Error in value[[3L]](cond) :
…
EAC-T updated
2 years ago
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Dear developers,
thank you very much for a great package that circumvents well known pitfalls in DEG calculation along pseudotime.
I have a dataset with 4 relevant biological lineages. What woul…
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it is a very dramatic and fantastic package that almost rebuilds the whole knowledge system of beginners!
However, there are a few questions I feel uncertain about and want to discuss with the author…