Finding RNA genes associated with X protein expression in CITE-seq Seurat object
Hi everyone,
I’m working with a CITE-seq dataset using Seurat. In the ADT (protein) assay, I see that some cells express the protein marker X while others don’t.
What I’d like to do is find RNA genes (from the RNA assay) that are associated with the X protein expression levels
Has anyone done something similar or could suggest best practices or tools for correlating continuous ADT vs RNA ?
Thanks a lot for your help !
• 6,392 views
•
link
updated
by
Kevin Blighe
•
written
by
Picasa
•
written
by
Picasa
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Analysing CITE-seq data where only 4 samples are CITE-seq and rest 11 are scRNA-seq
written by Sagrika •
-
Subset Seurat Object based on metadata
written by Nona •
-
10x GEX and ADT data analysis in Seurat
written by gdfsnkfns •
-
Options for assigning cell labels to barcodes from CITE-seq experiment
written by Chris Dean •
-
What controls splicing to switch from CD45RA to CD45RO isoforms ?
written by Alexander •
-
How much RAM for scRNAseq 200K cells?
written by psm
-
How to make a subset based on protein expression from CITE-seq data using R
written by yang.zhizhang •
-
Surat object UMAP - highlight cells based on Citeseq data
written by chi.delta •
-
How to concurrently filter RNA and CITEseq data within seurat object
written by cook.675 •
-
Subtract two RNA-seq datasets
written by Milos Pjanic •
One way would be to make a correlation test between every pair of gene-ADT, and test for significance. Another would be to run something like WGCNA and filter for pairs that end up in the same module. Just thinking aloud, not done exactly this myself so far. Pseudobulk would probably be preferred if possible.