Your videos are awesome! Yo have helped me a lot with my projects
@Collection_of_online_tutorials
Жыл бұрын
library(Seurat) library(tidyverse) library(patchwork) options(Seurat.object.assay.version = "v3") options(Seurat.object.assay.version = "v5") # Load in three GSE healthy donor sequencing data GSE128033
@user-ih2ku8wn5i
11 ай бұрын
Thank you for your great video!
@jesuchristopherjoseph3884
6 ай бұрын
Hi Nice tutorial. I have a question. You have done merge and followed by split on the object data. Is there any advantage of doing that? . In some tutorials they perform the normalization , PCA and Umap on the merged object and visualize the merged object before splitting? whats your thought?
@sreejas1302
Жыл бұрын
Hi Sir, Thank you so much for the wonderful video. And how to extract the correlation coefficient values from the integrated seurat object by CCA integration?
@sue8302
3 ай бұрын
Hi, if I would like to recluster cells of a particular cluster after integration, do I used similar reduction as the one in the integrated data? for example: cluster2
@Collection_of_online_tutorials
3 ай бұрын
you subset the cluster as a new object, then you can do any analysis you want to do, the reduction type will be the same as the main object
@denggool2
Жыл бұрын
I would appreciate it if you would upload a lecture on how to use cellchat to see the interaction between cells. !
@Collection_of_online_tutorials
Жыл бұрын
I am preparing NicheNet videos at the moment, it has similar function as cellchat, could make cellchat after NicheNet
@Collection_of_online_tutorials
Жыл бұрын
Network and signalling pathway analysis is next step of analysis after cell clusters and DEGs identification.
@denggool2
Жыл бұрын
Thank you for your teaching! I have a question.
@saleenayounus7797
2 ай бұрын
Dear professor could you make a video including doublet, integration, cell identification and cell interaction together in one video for any dataset based on contro and disease state
@cetanone
8 ай бұрын
thanks a lot, that's a nice explanation :)
@saleenayounus7797
2 ай бұрын
Dear professor one doubt, Here you applied SplitObject function after merging the multiple sample and then you done normalization in more than one samples. In another tutorial of yours, "Analysing More Than One Dataset" , you didnt apply SplitObject function after merging. Could you clarify it
@Collection_of_online_tutorials
2 ай бұрын
V5 save data in layers then you can perform dataset integreation. If you have a previous V4 object, then you need to slpit the V4 object into layers as a V5 object. Here I tried to demostrate how you start from a V3 or V4 object and then analsye in V5. The recent video for V5, I loaded three objects seperately, so the data are in layers. Is this clear to you? If you have V5 installed, just need to follow the recent one
@saleenayounus7797
2 ай бұрын
Got it. Thank you professor. I have another doubt . In my data set after integration, I removed the doublet using doubletFinder. My doubt is, after removing doublet data from the integrated data set, again we need to perform integration.
@__ASN__
6 ай бұрын
Hi, very nice tutorial. I have one question. After integration, does a new PCA need to be performed?
@Collection_of_online_tutorials
6 ай бұрын
no, the intergration acturally run a PCA like analysis
@navyav.b8572
4 ай бұрын
thank you for this video and it was really helpfull..one doubt is that.. which integration method is best .. and is there any specific normalisation step needed to be done like SCT..
@Collection_of_online_tutorials
4 ай бұрын
harmony has been consided as one of the best
@Collection_of_online_tutorials
4 ай бұрын
you don't need to run a normalisation step before SCT, SCT is an improved normalisation method
@navyav.b8572
4 ай бұрын
So after sct .. should we have to perform harmony integration . Is that the best solution
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