Hi everyone,
I've done single cell RNA-seq data analysis using Seurat. Now if I have 2 samples, a wild type and a mutant and I want to find out if any new cell populations appear or any cell population disappears in the mutant, how do i test for it ?
I looked at this tutorial and it explains integration and finding differences in gene expression and identifying DEG across conditions, but not to check if there are any new populations appearing. What is the best way to do that ?
1 answer
You identify your clusters. Then you check the proportion of each sample within your clusters. It' unlikely that you will have a cluster completely unique to one sample. However, you may have a cluster that is, for example, 20% of one sample, but only 1% of the other sample. Thus, that population is enriched in the first sample.
Log in to answer this question.
-
Merge or integrate multiple samples and then do downstream analysis
written by diqixiaoyaoer •
-
SCT transform
written by Nodilan •
-
scRNAseq for mutant and wt does not reveal differential expression of knocked-down gene
written by samuel.storey •
-
Difference between Seurat standard integration workflow and Seurat reference-based integration
written by mvis1231
-
SingleR for integrated scRNA-seq analysis
written by mvis1231
-
Seurat integrated analysis - methods for cell-type specific responses
written by jomo018
-
a question about the analysis pipeline in SEURAT3, with HARMONY, LIGER, etc
written by Bogdan
-
a question about filtering and integrating data in Seurat3
written by Bogdan
-
Seurat DefaultAssay "integrated" or "RNA" with integrated dataset????
written by cook.675 •
-
scRNA-seq analysis of two data-sets
written by piyushjo
