Introduction to spatial sequencing data analysis
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- Опубликовано: 28 авг 2022
- I show how to find, load, and process 10x genomics visium data. But I also explain how to load in spatial data from other platforms. This is useful if you want to analyze your own spatial-seq data, or supplement your project with analysis from already published data. I do this in python using scanpy.
Notebook:
github.com/mousepixels/sanbom...
Reference:
Murthy et al., Nature 2022
www.nature.com/articles/s4158... 
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Thanks for your time and effort.
Happy to help!
Amazing video! Awaiting your video on SquidPy!
By the time i do it there may be something even better xD
@@sanbomics ahaha yeah the field is evolving soo rapidly!
Your videos have been particularly helpful and I sincerely hope that you will consider doing a full video on the project of single cell rna analysis, similar to reproducing the Bioinformatic diagrams of some of the articles, which could help people to really understand how to interpret the actual problem.
I take the liberty of bothering you and sincerely hope that more and more people subscribe to your channel
The reason I didn't have a video this week is because I decided to make a full single-cell rnaseq analysis video! Its at like 1+ hours so far and growing haha. Hopefully people will actually watch it! I'm doing almost exactly that. I found an interesting paper and I am reproducing some of the figures/analyses
@@sanbomics wow! I can’t wait to see it !!!!
I'm glad someone is! I'm a little worried that people wont click on a two hour video haha. But.... I'm gonna go for it xD
@@sanbomics Haha, I believe your 2 hour video can really help people a lot , thanks for your effort again
I managed to keep it to only 1 hour 18 min xD ruclips.net/video/uvyG9yLuNSE/видео.html
thank you, it is very useful
You are welcome!
Hello! I am curious if you will have a much expanded version of the Spatial Seq Data analysis, also curious if there is any Proteomic analysis tutorial coming up! Thanks for your great work!
I might do a visium HD and/or a xenium tutorial soon but i have a lot of things in the queue and not enough time xD
@@sanbomics Visium HD would be amazing! I´m new to spatial transcriptomics and my first project is on visium hd data, am desperately looking for a nice workflow of analysis
Great video! How to annotate the clusters or the cell types?
I would say you can do it similarly to typical single-cell data. But just be aware that each spot is likely 5-20 cells. There are deconvolution methods you can look into as well that are supposed to break those into the individual cell types. Of course no deconvolution will be 100% biologically accurate though
Thanks for the great video. Could you please tell me how to convert a spatial seurat object into a scanpy for an integrated seurat object (two images)? Also, how should I handle these images in scanpy?
Something which will be nice is an analysis between sections. Let’s say one spatial image before and after drug treatment
Thank so much, I am performing Merfish (vizgen) analysis. Do you know when do we integrate all the samples toguether?
Before normalization? after normalization of each sample but before PCA?
thanksss
Can you make a video about spatial seq analysis on RStudio?
Unfortunately, unless there is a new tool that is specific to R that I want to try, I may not :(
@Question:
have done 10x spatial transcriptomics, and downstream analysis i try to use R, but the R generated UMAP (dim=30) is different from the UMAP that I se from the same data in the Loupe browser. I have played wtih the dim= 5, 10, 20, 30, still different?
Any comment would be helpful.
bthw: nice tutorial
@Sanbomics Have you tried with Spatial-seq data using stereopy
It would be great to got through, if you have a tutorial.
I haven't, but I will keep this in mind if i ever do!
Did you get an opportunity to do a follow up video where you demultipex each spot and use the squidpy package?
Not yet! I fear that by the time I do they will already have true single-cell spatial resolution xD (well there are some ways to do it already but its not mainstream yet)
@@sanbomics what ways can you do it already? do you mean different technologies and not the Visium?
Yeah there are different ways than Visium. Even 10x has a new method coming out with higher resolution. They just aren't mainstream commercialized yet
@@sanbomics What is the current best method to demultiplex each Visium spot or analyse 2 portions of the same Visium image? cheers
Also can you make a video which you explain all the elements of a seurat object
I've thought about it. chatGPT might do a really good job at it!
This is documented online in plenty of places
Do you have a code for doing the same in R studio, I've been trying to built a Seurat object with public available data, using the counts, position and images, with no success. Thanks
Sorry :( only code for this in python atm. What step specifically are you having trouble with? The initial loading of the data?