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.