Warning message: package ‘DESeq’ is not available for Bioconductor version '3.14'

csglab / REMBRANDTS

REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability

GNU General Public License v3.0

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Warning message: package ‘DESeq’ is not available for Bioconductor version '3.14' #9

Open LXsasse opened 1 year ago

LXsasse commented 1 year ago

Hi, It looks like Bioconductor got rid of DESeq. Is there a version of Rembrandts that uses DESeq2? Unfortunately, changing the library from DESeq to DESeq2 doesn't just work because the function "newCountDataSetFromHTSeqCount" is not contained in DESeq2.

rached-97 commented 1 year ago

Hi Alexander,

I modified the code some time ago to use DESeq2, I'll merge with the main branch shortly.

LXsasse commented 1 year ago

Thank you! That would be really helpful.

rached-97 commented 1 year ago

The new code's been merged. Please give it a try. Apologies for the delay.