Hello! I am a beginner at RNA seq analysis, I was hoping someone would point me in the direction of how I can take a data set (~50K genes in rows + 200 cells in columns, I have gene counts), perform a differential gene expression analysis (i don't know if this is needed for a PCA) and subsequently a PCA, allowing me to visualize using a tSNE plot (with something like rTsne).
(all this using R would be great)
I apologize in advance if I am asking redundant or senseless questions!!
(codes would be helpful)
Thank you!!!!
2 answers
Hey just wanted to come back and thank noorpratap.singh and @seidel for starting my journey with scRNAseq analysis, a long time has passed (>5 years, 1 PhD and post-doc later). I spent countless nights teaching myself how to perform scRNAseq analysis and I have now published in top journals including PNAS, Cell Reports, and others, now I teach scRNAseq analysis. Just goes to show how a little bit of guidance can change someone's trajectory. We all start somewhere, this is my beginning. Thanks guys.
Hi, Have a go through this link http://satijalab.org/seurat/
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I already have a csv file of genes and counts for my selected cells, How should I proceed??
@noorpratap.singh is telling you to walk through the Seurat tutorial, as it is a good instructional reference/discussion using R on the things you would like to do.