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aertslab / RcisTarget

RcisTarget: Transcription factor binding motif enrichment
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hg38 region databases? #13

Closed hypercompetent closed 2 years ago

hypercompetent commented 5 years ago

Hi Aerts Lab,

Thanks for the excellent cisTopic and RcisTarget packages! I'm applying them to some immune cell 10x ATAC-seq datasets, and I really like the analyses you've built around LDA.

Unfortunately, all of our analysis - both for ATAC and RNA-seq - are being performed against hg38, and it looks like there are only TSS-centric cisTarget databases for hg38.

Would it be possible to get hg38 versions of the genome-wide region databases as are available for hg19?

Cheers, -Lucas

s-aibar commented 2 years ago

Dear @hypercompetent ,

We will publish the databases for hg38 shortly.

However, there is also a tutorial on how to create new databases with any settings you might need: https://github.com/aertslab/create_cisTarget_databases