Grim Woo

Hi, thanks for development of such a nice package. Here, I wonder wether could I downloading atlas svg with selected region colored in purple like website. In [website](https://atlas.brain-map.org/atlas?atlas=138322605#atlas=138322605&plate=112282731&structure=10467&x=102726.07638888889&y=45298.939887152774&zoom=-7&resolution=138.29&z=3), we could...

How to install KlugerLab / FIt-SNE for Seurat usage in Windows 10 system ? I recently want to use this tSNE method to classify my seurat object. And I find...

root cell or milestone not provided, trying first outgoing milestone_id

1

thanks for developing such a magnificent software . here i encounter a problem : i set one cell as root (start ) according to [tutorial](https://dynverse.org/users/3-user-guide/5-adapting/) ```model_rooted % add_root(root_cell_id = Root.cell.id)```....

Thanks for development of such a good package. I am a new user for Monole 3. Here, I successfully create a trajectory plot according to [your guidance](https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/#learn-graph). However, error happened...

Thanks for developing this great software, and I have successed in velocyto plot in the original data. However, when I subset part of the data, the show.velocity.on.embedding.cor() shown no arrow....

RNA isoform/alternative splicing analysis

5

Hi, [Kallisto/BUSTools was recommended by Seurat](https://github.com/satijalab/seurat/issues/2813#event-3222404304) to perform RNA isoform/alternative splicing analysis. However, I didn't find the related workflow and found nothing in GitHub with the key word "isoform". This...

plot_genes_branched_heatmap with no reaction

3

thanks for developing such a magnificent software . here i encounter a problem : i want to plot the heatmap of genes of branches using ```plot_genes_branched_heatmap(monocle.tdcds,branch_point = 1,num_clusters = Num_clusters,cores...

verbose function in nmf()

1

Hi, I wonder if there was any parameter like "verbose = TRUE" to display a progress bar for nmf() procedure. Because it takes 12 hours to run nmf() without any...

"colors" setting in "add_track"

5

Thank you for the development of Plot1Cell. This issue is related to [issue #6](https://github.com/HaojiaWu/plot1cell/issues/6). Here, I set the collor for `plot_circlize` and `add_track`. The `plot_circlize` works perfectly. But the `add_track`...