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Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
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getGenePositions() in CONICSmat can not deal with gene names in ENSEMBL format #15

Closed biobug16 closed 4 years ago

biobug16 commented 4 years ago

Hi soerenmueller, I am trying to use 10X data where my filtered matrix has gene names in ENSEMBL format. Going through the CONICSmat pipeline I found getGenePositions() can only accepts the vector of genes in HUGO format. Can you please guide how should I troubleshoot this issue. Thanks

soerenmueller commented 4 years ago

Hi,

here is some code that allows to convert ensembl to HUGO with the biomart package:

https://bioinformatics.stackexchange.com/questions/2384/ensembl-id-to-genesymbol-with-biomart

Hope this is helpful.