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Dear Authors,
I used tradeSeq for my monocle3 object to find DEG of various lineage along trajectory. Output provides gene names, waldStat, pvalue and meanLogFC.
This is my first time doing tr…
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Hi,
CCPE is a useful tool to compute cell cycle pseudotime using single-cell RNA-seq data with ground truth. I also found that the paper described that CCPE could be used to analyze datasets without …
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I am running the basic pipeline (scvelo 0.3.1), starting from an AnnData object:
Preprocessing
scv.pp.filter_and_normalize(
adata_maca_10x, min_shared_counts=20, n_top_genes=2000, subset_high…
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Hi, I'm using plot_genes_in_pseudotime() but I'm not getting the expression trendlines I see in other plots. Here's an example:
```
plot_genes_in_pseudotime(pp, label_by_short_name = F, color_cells_…
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Hello, I have problem to understand properly the scale of the pseudotime heatmap going from 2 to -2,
after selecting genes with a menlogFC >=1 and p.adj
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Dear all,
I tried to plot genes that changed expression over pseudotime and I got a plot that all dots are on the x-axis, the plot and code are as follow:
`plot_genes_in_pseudotime(cds_order_1["CSN3…
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```
visCluster(object = ck,
plot.type = "both",
add.sampleanno = F,
markGenes = sample(rownames(mat),30,replace = F))
```
求问大佬,pseudotime热图绘图报错原因
![image](https…
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Dear Lamian team,
Thank you very much for creating this tool, it looks really promising and useful for my analysis. However, I am facing an error.
I am studying the gene expression over time from …
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Hi, I worked on PBMC dataset (T Lymph, 950 genes after filtering). Based on stream plot of velocity, I can see the arrows point from naive T cell toward memory & effector T cell. But pseudo-time plot …
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Hello,
I generated a UMAP trajectory in Monocle3 and am able to plot any genes of interest across pseudotime no problem with plot_cell_trajectory. However, we would like to be able to discover new …