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snikumbh / archR

archR: Identifying promoter sequence architectures de novo using NMF
https://snikumbh.github.io/archR
GNU General Public License v3.0
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Chromosomal Coordinates #6

Open ankushs0128 opened 3 years ago

ankushs0128 commented 3 years ago

Hi ,

I stumbled upon your package and it seems quite useful. I have quite a few files containing chromosomal coordinates and would like to check the regulatory elements within those chromosomal coordinates, Will it be possible to utilize the package for the analysis?

Best Ankush

snikumbh commented 3 years ago

Hi @ankushs0128 , It should be possible to use archR for your case, but note that the sequences should be of same length and it is preferred if the genomic regions are aligned/alignable e.g. as is possible with CAGE or ChIP-nexus. In this case, 'stability'-based model selection* can be used.

On the other hand, if the data is not precisely aligned/alignable such as with ChIP-seq, at the moment one can use 'cross-validation'-based model selection*. While I know that this works, I haven't yet extensively tested/checked this particular case.

If I may ask, the coordinates that you have are from which experiment?

You can give archR a try and let me know if you have any questions/feedback. I would also like to hear if it works well for your case.

*See argument modSelType here

snikumbh commented 3 years ago

Hi @ankushs0128 , eager to know if you ended up giving archR a try. Let me know how it did or did not work and/or if you have any feedback. Thanks.

snikumbh commented 2 years ago

Ping @ankushs0128 Sorry to bother you. Just wanted to check if you did try archR and if yes, how did it go.

Also, perhaps you may be interested in the recent most version which has additional improvements handling/avoiding identification of overfit clusters.

Cheers

ankushs0128 commented 2 years ago

sorry for the late reply,

Haven´t tried thereafter.

On Mon, Nov 8, 2021 at 6:59 PM Sarvesh Nikumbh @.***> wrote:

Ping @ankushs0128 https://github.com/ankushs0128 Sorry to bother you. Just wanted to check if you did try archR and if yes, how did it go.

Also, perhaps you may be interested in the recent most version which has additional improvements handling/avoiding identification of overfit clusters.

Cheers

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