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Hi, I have applied the same slingshot analysis to several datasets of the same cell type, using commands outlined in the vignette, Section 5. I am running version 1.4.0, other package versions detaile…
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Line 122: ordering_genes not defined.
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Dear developer,
I installed the "conditions" branch. I ran `slingshot` with `seurat` object and got nice trajectories. Then I would like to use `tradeseq` to find differentially expressed genes bet…
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Hi everyone,
Thank you so much for creating slingshot!! It's the best for my data so far.
I have a SEURAT object and I followed the tutorial and did this:
sds
EAC-T updated
3 years ago
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Hi,
Is it possible to subset clusters and then draw pseudotime trajectory?
I tried subsetting my dataset to focus on just the clusters I want to represent, but I get the follwing error.
`cds_sub…
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Hello,
I'm new to coding and very new to tradeSeq, and I was hoping to get some help here.
I am working on a sc-RNA-seq data that was available online and already pre-processed (normalised) - I on…
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Just curious if there is a way to integrate UMAP and cluster analysis obtained from Seurat for pseudotime analysis using this package
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Hi,
I would like to get some advice on selecting the appropriate clustering method for the Slingshot analysis. My goal is to infer the trajectory of progression (and potentially bifurcations) from …
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Hi Volker,
First, thanks for the package and a lot of interesting discussions here! We are working with a dataset of about 700 cells, after filtering we have about 600 genes, 70 of which are then p…
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I have single cells from three different real-time timepoints. Instead of inputting a genes for ordering all of these cells along pseudotime, is there a way to specify one time-point as the beginning …