Matt Thornton

oops. I think this is the question I asked. I will try to make a linseed object with a matrix of the RPKM for the set. The original idea was...

Hello! I messed up and accidental upgraded "conda upgrade all". I have downgraded, but I'm still getting this error: ``` Error in py_get_attr(x, name, FALSE) : AttributeError: module 'umap' has...

Hello! Absolutely. Thank you! ``` library(Signac) library(Seurat) library(AnnotationHub) library(BSgenome.Hsapiens.UCSC.hg38) library(dplyr) library(ggplot2) library(patchwork) library(reticulate) use_python("/home/met/.conda/envs/r-reticulate/bin/python3") # This will get the proper version of the Ensembl for your data hub

So I did notice that it is really really close to 1 and if I set the filtering blacklist_ration < 1.015. I still get most of the clusters that I...

I also used the gencode genome fasta with cellranger-arc genomeGenerate. I had read somewhere that the differences beyond having a "chr" were that UCSC style begins on '1' and Ensembl...

Is it because the default assay was set to "SCT"?

Hello! When I change the DefaultAssay to 'RNA'. The error goes away. However, you get a mismatch error, 1: Different cells and/or features from existing assay SCT. So I guess...

Hi Sahar There is a function to prepare SCT objects for FindMarkers [PrepSCTFindMarkers] That you may need. This worked for me. Ioaded each object trom rds files. ``` ws_set