Standard scRNAseq preprocessing workflow with Seurat | Beginner R

[@jajaja20703]

Great video! Would love to see more of the story and have a more advanced analysis of this dataset!

[@keshavprasad6485]

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.

[@biostatsquid]

Thank you so much for your feedback Keshav! I am glad you liked it and thanks for those great ideas on new topics!

[@mlu213]

Really great tutorial! Any chance you could make that short tutorial about the structure of a Seurat object for beginners?

[@huyquach5044]

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.

[@biostatsquid]

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!

[@ambrosia9094]

Keep teaching very helpful 🙏

[@mortezahadizadeh9637]

I greatly appreciate your tutorial.

[@davidguardamino]

amazing video!!! thank you so much!!!

[@苏峰-p6v]

Great video! thank you so much!!!

[@puspendughosh9573]

Kindly make a tutorial for monocle3 & trajectory analysis using 10x genomics data.

[@hossein37]

Thank you

[@mihacerne7313]

Squidtastic!

[@thedizzyyak]

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!

[@OsamaElghawil]

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

[@poojaparis]

Do you use dropletutils for selecting single cells?

[@biostatsquid]

Hi Pooja, thanks for your comment! I haven't used dropletutils to filter our doublets, more recently I switched to DoubletFinder if that helps!

[@fred-w4b]

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

[@biostatsquid]

Hi - depends on how big your dataset is - but yes, I ran it on a PC machine, 16GB.

[@sanjaisrao484]

Mam, Rstudio crashes if I use ScaleData function, what to do 😢

[@biostatsquid]

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!