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I recently downloaded the demo Harmony notebook just to see how it worked. I noticed that after running the `palantir.plot.plot_palantir_results()`, while the pseudotime looked correct the entropy gra…
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Hello,
Upon running URD on our data, we notice a jump between our root cells at zero and the next lowest pseudotime value. This seems to be typical (Siebert et al., fig 3D). Attached an image of ou…
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [ ] (op…
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Hi everyone,
First, I would like to thanks you for the work on the pre-print paper and the shinny app which is really useful.
I'm here about a method that you used in the benchmark : Waterfall. …
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when I run the following code in monocle3:
plot_genes_in_pseudotime(cds[Track_genes_sig,], color_cells_by="pseudotime",
min_expr=0.5, ncol = 2)
always return the error…
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Hi, I tried to use[TrAGEDy](https://github.com/No2Ross/TrAGEDy), the I performed analysis on the dataset and generate two trajectories, when I used the TrAGEDY to compare the two lines, I found the NA…
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非常感谢junjun老师的优秀工具!
想请教一个问题:在对接分析monocle3得到的cds文件时,
mat
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Dear John and developers,
I find your tool super interesting. I have a single cell data set with 12 time points that I managed to reduce to 4 thousand cells to be able to run DeLorean (I understand…
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Sorry for posting this again, but unfortunately the previous thread was closed and I could not comment there. I want to create a heatmap of features along a DPT pseudotime (see attached panel below fr…
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Hi,
many thanks for developing and maintaining this very cool tool! We could already obtain some very nice insights using sciCSR! However, as you pointed out in your tutorial using SHM as mode for …