Seurt Rename Orig.ident

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3.3 years ago

clizama • 0

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I got this dataset from geo and was all in one mtx file and I was wondering if is possible to change the orig.ident and group It into controls and diseases.

For Example: Group F00202-F01394 to Control, ILd53-63 Disease1, HD65-HD70 Disease2

Thanks

Seurta cell RNAseq Single • 3.2k views

ADD COMMENT • link updated 3.3 years ago by ATpoint 85k • written 3.3 years ago by clizama • 0

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Do you have the information which cells belong to control and disease, so is this a question on how to use Seurat for renaming or on how to identify which genes are control and disease?

ADD REPLY • link 3.3 years ago by ATpoint 85k

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I have the mtx file and the excel file from the geo database to know which sample correspond to control or disease. The problem is theey upload just one mtx filefor all the samples. The other datasets I was using each sample has his own mtx files and is easy to group.

ADD REPLY • link 3.3 years ago by clizama • 0

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So it comes down to changing some annotations? See https://satijalab.org/seurat/articles/essential_commands.html and https://github.com/satijalab/seurat/issues/1966

ADD REPLY • link 3.3 years ago by ATpoint 85k

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