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Standard scRNAseq preprocessing workflow with Seurat | Beginner R 

Biostatsquid
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In this tutorial we will go over the basics steps of preprocessing for single cell RNA seq data in R using the Seurat package.
With this step-by-step guide you will learn the standard pipeline using the Seurat package, which is very common in transcriptomics analysis. We will go through the basic steps of quality control and filtering, normalisation, identification of highly variable features (genes), clustering and different dimensionality reduction methods (PCA, UMAP…).
Hope you like it!
Link to dataset: www.10xgenomics.com/resources...
Step by step explanation: biostatsquid.com/scrnaseq-pre...
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If you liked this video or found it useful, please let me know! Your comments and feedback are very much appreciated😊
If you have questions, don't hesitate to leave me a comment down below, I will answer as soon as I can:)
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Other interesting resources for scRNAseq preprocessing:
A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines: www.sciencedirect.com/science...
Amazing step-by-step tutorials and scRNAseq analysis workflows with Bioconductor:
www.singlecellcourse.org/scrn...
bioconductor.org/books/3.16/OS...

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17 июл 2024

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Комментарии : 19   
@jajaja20703
@jajaja20703 Год назад
Great video! Would love to see more of the story and have a more advanced analysis of this dataset!
@mortezahadizadeh9637
@mortezahadizadeh9637 Год назад
I greatly appreciate your tutorial.
@user-mw2pf8tw6c
@user-mw2pf8tw6c 6 месяцев назад
Great video! thank you so much!!!
@keshavprasad6485
@keshavprasad6485 Год назад
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
@biostatsquid Год назад
Thank you so much for your feedback Keshav! I am glad you liked it and thanks for those great ideas on new topics!
@ambrosia9094
@ambrosia9094 7 месяцев назад
Keep teaching very helpful 🙏
@huyquach5044
@huyquach5044 Год назад
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
@biostatsquid Год назад
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!
@hossein37
@hossein37 Год назад
Thank you
@mlu213
@mlu213 4 месяца назад
Really great tutorial! Any chance you could make that short tutorial about the structure of a Seurat object for beginners?
@mihacerne7313
@mihacerne7313 Год назад
Squidtastic!
@puspendughosh9573
@puspendughosh9573 Год назад
Kindly make a tutorial for monocle3 & trajectory analysis using 10x genomics data.
@user-il4jz8mu6o
@user-il4jz8mu6o Месяц назад
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
@thedizzyyak
@thedizzyyak 5 месяцев назад
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!
@poojaparis
@poojaparis 9 месяцев назад
Do you use dropletutils for selecting single cells?
@biostatsquid
@biostatsquid 9 месяцев назад
Hi Pooja, thanks for your comment! I haven't used dropletutils to filter our doublets, more recently I switched to DoubletFinder if that helps!
@sanjaisrao484
@sanjaisrao484 Год назад
Mam, Rstudio crashes if I use ScaleData function, what to do 😢
@biostatsquid
@biostatsquid Год назад
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!
@davidguardamino
@davidguardamino 9 месяцев назад
amazing video!!! thank you so much!!!
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