scRNAseq analysis on multiple datasets
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SG • 0
@2efa9769
Last seen 26 days ago
India

Hi all, Kindly guide me. I am a beginner, exploring scRNAseq analysis. I want to combine different scRNAseq studies on various tissue to find how gene profile changes in all of them. For example - Altered Gene Expression Profiles in the Brain, Kidney, and Lung of One-Month-Old Cloned Pigs

So here my scRNA seq data say hypothetically be-

gse ... brain dropseq year 2015

gse..... kidney 10x chromium year 2017

gse..... lung 10x year 2019

These studies- a)Have been performed by different researchers b)Different libraries c)Same Model organism -pig but different species and age

There would be much batch effect due to different libraries and location and year etc of processing. I want to combine them to see how the gene /transcript abundance changes.

Q1- Would you please help me to tell which packages I could use for QC and removing batch effects with respect to this study? Q 2- Would you please suggest some tutorials etc on Bioconductor with a similar problem? Q3- With so many packages how to choose which will best fit our analysis any tips?

Any other suggestions regarding this are also invited.

Thanks!

scRNAseq • 125 views
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I think this will be of interest to you: https://bioconductor.org/books/release/OSCA/

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You want to see how gene expression changes in completely different tissues? Is there any kind of gene atlas for your organism? You can't fix the batch effects. It is impossible to meaningfully compare these totally different samples, and I don't see why you'd want to. Brain is way different than kidney.

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