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Thank you for what appears to be an excellent introductory tutorial, however could you assist in including instructions on how to actually access the DS1 and DS2 practice data you use. You begin by making a Seurat object of data but no instruction on how you uploaded the data;

Thanks for the great tutorial.

Everything runs well up until
cl_markers %>% group_by(cluster) %>% top_n(n = 2, wt = avg_logFC)

I think something may have changed such that it should have wt = avg_log2FC, which runs fine.

Thank you for the excellent and very comprehensive tutorial !
I would like to know one specific thing about RNA velocity. In the tutorial, it is mentioned that the second case (of batch corrections) becomes important for RNA velocity analysis and I was wondering if you have any guidance on how to carry out such analysis. For instance, I've sc-RNAseq data coming from multiple batches which is then processed to get a batch-corrected cell state clustering. Now, for the RNa velocity, I've generate 6 loom files (each coming from a different batch) using velocyto package and I combine them together and then finally merge the combined loom file to the processed Andata object. Is this the right approach or do I need to be careful about batch corrections when combining individual loom files ?

Dear all,
I am running Seurat in a R environment created in conda. I am following Seurat tutorial to analyse my data

library(Seurat)
library(dplyr)
library(patchwork)
library(ggplot2)

After reading the data, and creating Seurat object, I am doing some QC.
When I run

plot=VlnPlot(Mydata, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
plot

I do not get any Figure window or any plot. Is there a package I am missing to install?
Thanks for your help.