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Hi there,
thank you for having developed this tool.
i'd use my data (60k cells) analysed with seurat v3 in scorpius. it' possible analyse this large dataset with our tool?
any suggestion for how ex…
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Hello,
I am running fitGAM with parallelization on counts from an object with 11,768 cells and 26,152 genes on a machine with 16 cores and 256 GB of RAM:
BPPARAM$workers
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Hello! I have an integrated Seurat object (R 3.5.1, Seurat_3.1.5) which I am trying to use with SeuratWrapper's Monocle3 trajectory analysis (R 3.6.1, Seurat_3.1.5). Following the [tutorial](https://h…
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Hi, I am experimenting with a docker-base setup of training sessions. Given that your package has been shown in our latest course, it tried to get the [script](http://data.bits.vib.be/pub/trainingen/s…
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Hello! I recently started getting in to using PHATE. I am wondering if one can color the cells on PHATE scatter plot by pseudo-time instead of a gene or known time-points across the data. Similarly, h…
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Hello,
I started with the same issue as #32, but after correcting the sparse matrix problem I get another error:
```Error in Biobase::exprs(cds) : object 'cds' not found```
I am working with …
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Hi! I'm having some trouble making scatterplots in scvelo that show the velocity pseudotime, root cells and end points. Some days the line works without any problems, other days it gives a TypeError, …
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Hello,
Could it be possible to use pseudotime values to build a linked SOM of scATAC and scRNA?
I don't have multiple time points like in your paper, and I was wondering if it was possible to buil…
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Hi,
Thanks for creating this package. I'm planning to use this in many ways.
I have generated true counts using `SimulateTrueCounts` and got the kinetic parameters for each gene. I am wondering w…
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Dear Tim,
I noticed that the RunTF-IDF function had four methods to perform the LSI algorithm. After a full test of all four methods with the same scATAC data (around 7000 cells of 10X), I hap…