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reimandlab / ActiveDriverWGSR

ActiveDriverWGSR is an R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data
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GRCh38 reference files #3

Closed bkinnersley closed 4 years ago

bkinnersley commented 4 years ago

Hello,

Thank you for this very useful software package! I was just wondering if there are plans to add support for GRCh38, or if it would be possible to provide details for how other users could create GRCh38 reference files suitable for use with ActiveDriverWGSR?

Thanks very much

Best wishes

Ben

reimand0 commented 4 years ago

We have an unstable and unverified version of ActiveDriverWGS supporting multiple reference genomes, in a separate branch here: https://github.com/reimandlab/ActiveDriverWGSR/tree/genomeVariety. Work is ongoing to create an updated package in CRAN. Stay tuned!

bkinnersley commented 4 years ago

Thanks very much! It seems that currently the recovery directory option in this branch (https://github.com/reimandlab/ActiveDriverWGSR/blob/genomeVariety/R/ActiveDriverWGS.R) is not working as previously (https://github.com/reimandlab/ActiveDriverWGSR/blob/master/R/ActiveDriverWGS.R), I don't know if it is related to this commit https://github.com/reimandlab/ActiveDriverWGSR/commit/bdc341d3888ba002301a5a8ac720eaf0b8b9fbc1

reimand0 commented 4 years ago

Thanks for letting us know. will investigate. This fix is certainly quite cryptic.

On Mon, Aug 3, 2020 at 12:54 PM bkinnersley notifications@github.com wrote:

Thanks very much! It seems that currently the recovery directory option in this branch ( https://github.com/reimandlab/ActiveDriverWGSR/blob/genomeVariety/R/ActiveDriverWGS.R) is not working as previously ( https://github.com/reimandlab/ActiveDriverWGSR/blob/master/R/ActiveDriverWGS.R), I don't know if it is related to this commit bdc341d https://github.com/reimandlab/ActiveDriverWGSR/commit/bdc341d3888ba002301a5a8ac720eaf0b8b9fbc1

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reimand0 commented 4 years ago

Hi Ben, the new version 1.1.0 now supports human reference genome hg38 and mouse genomes mm9 and mm10. You can get it from GitHub (master) while CRAN review is in progress. Please let me know of any comments or findings. best, Jüri