Question: single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
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gravatar for DrAcula
2.5 years ago by
DrAcula40
University of Miami
DrAcula40 wrote:

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!!!!

rna-seq • 1.9k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by DrAcula40

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

ADD REPLYlink written 2.5 years ago by DrAcula40

@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.

ADD REPLYlink written 2.5 years ago by seidel7.1k
1
gravatar for noorpratap.singh
2.5 years ago by
University of Maryland
noorpratap.singh300 wrote:

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

ADD COMMENTlink written 2.5 years ago by noorpratap.singh300
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