single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA

Question

[DrAcula]

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!!!!

[DrAcula]

I already have a csv file of genes and counts for my selected cells, How should I proceed??

[seidel]

@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.

Answer 1

[DrAcula]

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.

Answer 2

[noorpratap.singh]

Hi, Have a go through this link http://satijalab.org/seurat/