It was an excellent explanative video. Thank you very much for your efforts. What I particularly like about your video is that you not only explain what is the next step to be done (along with the code) but you also explain the reasoning and the advanatges of implementing the particular step. Just alist of steps one can also find it in the respective seurat tutorial page but your explanations is I think the key differentiator between your work and other videos in this space. Please do keep them going. I would suggest that you could make a full series on scRNAseq, spatial transcriptomics , scATACseq etc.
Thank you very much for the video. It is so happy for me to know your channel. When you have time, please make a video for using WGCNA package. Thank you.
Thank you Huy! I have not worked with weighted correlation network analysis (yet!) but I'll write it down in my to-do list:) Thanks for the suggestion!
are you running this on linux? According to you video your max RAM should be around 8-10GB. I tried to run it on my mac with 18GB of RAM (nothing else opened) and it maxed out. I am surprised by how efficiently your machine handles the memory
Are you able to explain why a threshold of 2500 was used for the nFeature_RNA filtering? Looking at the FeatureScatter plot it is not obvious to me that this should be the cutoff. What is the reasoning behind 2500? Thanks for the video!
Hi Sanjai, it might be a memory issue. A quick search got me this which might help, but you might need another solution: community.rstudio.com/t/silent-memory-limit-exceeding-scaledata-from-seurat-causes-crash/17990 Hope you solve it!
Great video! Would love to see more of the story and have a more advanced analysis of this dataset!
It was an excellent explanative video. Thank you very much for your efforts. What I particularly like about your video is that you not only explain what is the next step to be done (along with the code) but you also explain the reasoning and the advanatges of implementing the particular step. Just alist of steps one can also find it in the respective seurat tutorial page but your explanations is I think the key differentiator between your work and other videos in this space. Please do keep them going. I would suggest that you could make a full series on scRNAseq, spatial transcriptomics , scATACseq etc.
Thank you so much for your feedback Keshav! I am glad you liked it and thanks for those great ideas on new topics!
Thank you very much for the video. It is so happy for me to know your channel. When you have time, please make a video for using WGCNA package. Thank you.
Thank you Huy! I have not worked with weighted correlation network analysis (yet!) but I'll write it down in my to-do list:) Thanks for the suggestion!
I greatly appreciate your tutorial.
Keep teaching very helpful 🙏
amazing video!!! thank you so much!!!
Really great tutorial! Any chance you could make that short tutorial about the structure of a Seurat object for beginners?
Thank you
Squidtastic!
Kindly make a tutorial for monocle3 & trajectory analysis using 10x genomics data.
How I can do interrogating the sample PBMC clusters for the following genes : CD68
CD45
Sox10
CD44
any similar video will be great ? thank you
are you running this on linux? According to you video your max RAM should be around 8-10GB. I tried to run it on my mac with 18GB of RAM (nothing else opened) and it maxed out. I am surprised by how efficiently your machine handles the memory
Hi - depends on how big your dataset is - but yes, I ran it on a PC machine, 16GB.
Are you able to explain why a threshold of 2500 was used for the nFeature_RNA filtering? Looking at the FeatureScatter plot it is not obvious to me that this should be the cutoff. What is the reasoning behind 2500? Thanks for the video!
Do you use dropletutils for selecting single cells?
Hi Pooja, thanks for your comment! I haven't used dropletutils to filter our doublets, more recently I switched to DoubletFinder if that helps!
Mam, Rstudio crashes if I use ScaleData function, what to do 😢
Hi Sanjai, it might be a memory issue. A quick search got me this which might help, but you might need another solution:
community.rstudio.com/t/silent-memory-limit-exceeding-scaledata-from-seurat-causes-crash/17990
Hope you solve it!
Great video! thank you so much!!!