Flu09

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': invalid format '%d'; use format %f, %e, %g or %a for numeric objects

1

Hello, I have an issue with my seurat object (around 1.5 million ). It is saved on disk using the BPCells package. The problem occurs on the RunPCA step. ```...

seurat findmarkers()

4

hello, thank you for making this great tool. I cannot seem to understand how to use it. I have differentially expressed genes from findmarkers() in seurat between diseased fibroblasts and...

Hello, i am new to the tool. I am familiar with seurat and limma package but as I understand it is available through muscat as well. I have gathered samples...

question about batch

10

Hello, I have 3 studies which I want to annotate using a built reference. I wonder if what I am doing is correct. I label transfered from the built reference...

pvalue or adj_pvalue

1

I used findmarkers() in Seurat to find DEGs I wonder which is the right metric to use pvalue or adj_pvalue

ENSEMBL

1

I am wondering if this tool works with genes with ENSEMBL IDs

hello, I have run Seurat's findmarkers to compare between genotype1 diseased versus healthy celltypes then between genotype2 diseased versus healthy celltypes then I used gseGO() to find the pathways for...

problem with gseGO()

1

``` gsea_BP_astro_33 0.05 before using gseGO() or keep all genes. I would appreciate it if you can help. Thanks.

how to generate the heat map plot of the modules ?

3

Hello, I often see this heatmap in papers. I am not sure how to generate something similar. Also How to generate the motif plots. Thank you. 

Different batches/studies

2

Can I run pyscenic on concatenated raw matrix from 3 different studies? or should run it run on each ?