best practices for single-cell analysis across more samples???

Question

[GiV17]

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

[biofalconch]

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

[GiV17]

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

[ATpoint]

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.