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I tried this:
> plot_genes_branched_pseudotime(HSMM_major[84,], branch_point = 1,color_by = "cell_class", ncol = 2)
and got this error:
Error in if (nrow(ancestor_exprs) == 1) exprs_data
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Hi,
I have imported a dataset I have analysed in Seurat into Monocle3 using the SeuratWrappers function as.cell_data_set and continued on to the pseudotime analysis in Monocle3 which worked well.
…
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Hi everyone,
I am analysing a single cell RNAseq (as seurat object) and I have a signature/list of genes (added as a module in the seurat Metadata with AddModuleScore).
I know how to use Monocle 3 …
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I am impressed by the described in your paper and am eager to explore the applications of the TFvelo in my research.
However, it doesn't show velocity very well in my adata, what parameters can be …
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Suppose that I would like to assess whether gene expression differs between two lineages of a trajectory, when I know the true pseudotime and posterior probabilities for each cell in the dataset.
Is …
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Dear all,
I would like to run monocle3 package with Seurat integrated data.
For this I used below command.
library(SeuratWrappers)
library(monocle3)
library(monocle)
pbmc3.cds
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Thank you so much for the great tool.
I just wanted to report an error that I encountered when running floodPseudotimeProcess function. I don't know why my obj.urd@diff.data hasn't been initialized…
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wondering how to generate this file for use with the genes_correlated_with_pseudotime.py script
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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…
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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,…