best practices for single-cell analysis across more samples???
Hi, I have 4 samples about a colon cancer condition, analyzed with Chromium 10X. Now I used Seraut v5. for single sample, but I have 4 samples and my focus is to investigate the cells in all samples. SO What is the correct procedure in this case? I find only in relation to individual samples. But when I have multiple samples of the same condition, how do you do it? I would like a best practices for single-cell analysis across more samples in the same condition. Help me Thanks all. G
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It would help if you were a little bit more specific. What do you mean relation to individual samples? I recommend going through the vignettes of Seurat first and try a few things For example: https://satijalab.org/seurat/archive/v4.3/integration_introduction
Thanks. I have 4 samples: S1, s2, S3 and S4. For each samples, i have the results of Cell ranger pipeline. The samples rappresent the same condition, the same tessue so for the paper, i would like to integrate the dataset. So how can ti do? What Is the best practices of more samples for scRNA??? THANKS
Read the Seurat, or Bioconductor (OSCA) or ScanPy, or https://www.sc-best-practices.org/preamble.html documents. Get a background first, then ask a precise question. Here you essentially ask people to repeat what is in linked documents.