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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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Saving SC3 clustering output as csv files #106

Closed bsamal20 closed 2 years ago

bsamal20 commented 2 years ago

I get beautiful graphs on gene expression, differential gene expression (DE) as well as marker genes marking each cluster. However, I would like to save these results as csv or Excel files to double-check with databases etc.

mhemberg commented 2 years ago

Thanks for your question. If you run SC3 in the non-interactive mode, I think it should be straightforward to extract this information as shown in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/SC3.html#de-and-marker-genes

bsamal20 commented 2 years ago

Working from the 'Yan' dataset was smooth. However, how do I use SC3 with my 10X Genomix data already normalized with Seurat, before or after running PCA?

bsamal20 commented 2 years ago

Running SC3 using yan dataset goes smoothly. How can I run my 10X Genomix data normalized using Seurat before or after PCA?