Saeed

Hi @cflerin , There are two outputs in the standard pipeline. 1) Adjacencies based on GRN. Here we see an 'importance' score for each target gene and Transcription factor relationship....

Hi, I have been trying to use the loom file generated by pySCENIC on ScopeLoomR to further manipulate it. The loom file generated by pySCENIC from a windows platform has...

Using MAGIC with a combined dataset

4

Hi, I have to combine several datasets. Batch correction is used for clustering and Dimensionality reduction. But for visualization and DEG analysis I will be using normalized RNA counts (Seurat...

Dear, Thank you for this tool. This has been incredibly helpful in assisting us to easily share the data with our wet-lab colleagues so they can explore on their own....

Details to be added about the available model

2

Dear, In the description of the model it is not clear whether the model involves cells from both healthy and CD or just healthy? I am especially referring to 'Cells_Intestinal_Tract...

** If this is a question and not a bug report or enhancement request, please post to our google group at https://groups.google.com/forum/#!forum/monocle-3-users** **Describe the bug** Vignettes load incompletely. A section...

Error after running parallel on HPC

1

Hi, I am trying to run the gsva on a seurat object with an assembled database form multiple origins. I already tested it with a subset of the seurat object...

Annotations.py fails- dependency on old sklearn modules?

4

Dear, I wanted to perform annotations locally or with our cluster. So I made a new conda environment and went with the script available (for colab session) at your website...

Hi, Thanks you for Scope and ScopeLoomR. I tried the following code to add the AUC_Matrix. The loom file works, but I cannot visualize any regulon activity in scope. ```...

add_seurat_clustering is not working

11

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