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Hi, I was wondering if I could use Libra (specifically with setting: de_family = "pseudobulk", de_method = "limma", de_type = "voom") with a scRNA-seq dataset (Seurat) in which I have let's say:
- Tw…
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- as per [Li and Redden (2014)](https://doi.org/10.1002%2Fsim.6344), using the standard sandwich variance-covariance matrix to perform a Wald test of significance - as we do in `waldtestGEE()` - leads…
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Firstly, thank you for putting together such a useful tool!
Apologies in advance if this is a naive issue as I am relatively new to R and scRNAseq analysis. I am trying to use Lamian to compare pse…
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This prevents labels from overlapping but would require a bit of re-working how the `pheatmap` call is made.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#mark-a…
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Hi Rongbin,
Thank you for providing such a useful tool. I've tested Mebocost on my personal scRNA-seq dataset, and it worked beautifully. I’m wondering whether you will include functions for direc…
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Hi Alex
I have a question regarding the output of STARsolo.
In order to process the results in a downstream analysis, I process the output files of the Solo.out folder with the Seurat package in …
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Hello,
I am currently trying to replicate data from this [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02302-5) using STARsolo.
In short they perform a SPLiT-seq expe…
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New projects (3):
1. [Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins](https://data.humancellatlas.org/explore/projects/a83b7f45-bfb1-4c…
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Dear SEACell team,
first of all thank you for such an interesting and versatile tool.
I have been recently using it for creating metacells from a scRNA-seq dataset with cells coming from differe…
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I was hoping to use CellOT on full scRNA-seq data and was wondering what the training times for that should look like and if there is any way to accelerate training. I'm currently running scGen to get…