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I recently started using monocle3 for pseudotime analysis. However, since I'm working on Jupyter on a computing cluster, I cannot use the order_cells() function interactively, and have to provide eith…
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At the moment, the x-axis seems to always be labelled with `pseudotime`, see line 15 & 16 in our basic tutorial, even though `latent_time` is specified. Can we change this, to make it more obvious wha…
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Hello,
Thanks for great tutorials, I am currently following your slingshot tutorial and I am running into an error when running the rand_forest line.
here is what I get :
model %
+ set_engine…
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Hello,
Thank you for the wonderful package, I am very excited to utilize it for my data sets!
I have created a cds object from an integrated Seurat object, but an having issues with calculatin…
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Hi! I'm trying to use Palantir to compute pseudotime and gene expression trends. Yet, I'm facing the following bug, which seems to be due to the deprecation of some syntax used in the code.
```
ge…
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Hi, Monocle is so useful for me, 3ks to you all.
But I got the "pseudocount" not found error when I use "norm_method = log" in "plot_multiple_branches_pseudotime".
Btw, I found the code "pseudocount…
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Hello!
Thanks for this wonderful pseudotime tool. Being a first time user, I am having difficulties in selecting variable genes using st.select_variable_genes() function. I am reading an anndata (.h5…
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The object would have counts in `assays` and the pseudotime and cell-level weights in `colData`.
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Hi,
I have been running into problems with ````associationTest```` results when a single lineage is fit. Specifically, results differ wildly when changing the number of knots from 4 to 5 in the ``…
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Hi all,
I am using Monocle 3 to analyze diff gene expression and to perform trajectory analysis in two samples: ctrl and treated cells.
First, I created a combined CDS file and I performed the de…