Export normalized matrix Scanpy
Hello, is there a way for me to export the normalized data frame using scanpy?
• 4,483 views
•
link
updated
by
Nitin Narwade
•
written
by
Skamboj •
•
written
by
Skamboj •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
DEA best practices: raw vs. normalized data
written by npont •
-
Differential Expression using Scanpy
written by Skamboj •
-
Transfer harmony-integrated scRNA-seq data to scanpy
written by fifty_fifty •
-
Extracting RNA sequence - single cell
written by Skamboj •
-
Co-expression of markers in single cells using scanpy
written by A.rex2 •
-
automatic clustering annotation using python
written by safeassli •
-
scanpy differential expression log fold change
written by Skamboj •
-
how to export scanpy data to loupe?
written by krorange •
-
How to export rld (rlog) or vsd values from DESeq2?
written by LuisNagano •
-
edegR, export TMM normalized method
written by lilingjoyo •
Did you try googling it?
There are a number of GitHub issues raising the same query. for example, this thread. It is for exporting raw expression matrix though, but still, if you tweak it a little bit and know the normalized data will be stored in the
layersattribute ofAnnData objectyou will be able to resolve your query by yourself.Do not delete posts that have received feedback. If you've managed to solve the problem yourself, please add an answer outlining what you did and accept it so others can benefit from your effort.