search

buenrostrolab / FigR

Functional Inference of Gene Regulation
https://buenrostrolab.github.io/FigR/
MIT License
31 stars 10 forks source link

runGenePeakcorr,Using the genomes of other species #8

Open liyang24 opened 1 year ago

liyang24 commented 1 year ago

Hi,

Thank you for the package. I'm not using human or mouse data, and I want to know if ### runGenePeakcorr this step supports the use of genomes from other species?

Thank you!

vkartha commented 1 year ago

Hi there - currently it only uses pre-existing genome builds for mouse and human (mm10 for mouse; hg19 and hg38 for human), which is used for both GC content determination and gene TSS annotations. These are loaded under the hood depending on what is specified by the user. If you want to use a different ref, it would need to have it's corresponding build as part of the BSgenome set of R packages, and you'd also need the RefSeq TSS gene annotations for it (which we built). We can certainly make both of these parameters that users provide as part of FigR in the runGenePeakcorr function, but it would need to be standardized in terms of the input formats expected. If I may ask, which species are you looking to run this on, just to gauge how simple this extension can be?

liyang24 commented 1 year ago

Hi We use the cattle data and expect to get the final GRN,I wonder if it is feasible

zhiyhu commented 1 year ago

Hi,

We are also very eager to apply FigR on other species - zebrafish in our case.

The relevant R packages are

Is that possible to build a customised genome for this pipeline?

Many thanks in advance!

Dalhte commented 1 year ago

Hello there I would like to apply FigR on the rat genome. I'm working on RN6. Is it possible to implement this genome too ? I have a customised BSgenome ( BSgenome.Rnorvegicus.NCBI.rn6) and I can build a RefSeq TSS gene annotations if needed. Best regards David