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ge11232002 / TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis
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2017 JASPAR DB #11

Closed akhst7 closed 6 years ago

akhst7 commented 7 years ago

Is there any way to import 2017 JAPSAR DB as a getmatrixset object ?

ge11232002 commented 7 years ago

You mean JASPAR2016? You can load all the matrices by 

getMatrixSet(JASPAR2016, opts=list(all=TRUE)
akhst7 commented 7 years ago

No. I have Jaspar 2016. I saw an update version (2017) of Japspar DB on the Jaspar web site and was wondering if I could update the 2016 DB somehow.

Thanks.

AKi

On May 29, 2017, at 5:30 AM, Ge Tan notifications@github.com wrote:

You mean JASPAR2016? You can load all the matrices by

getMatrixSet(JASPAR2016, opts=list(all=TRUE) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ge11232002/TFBSTools/issues/11#issuecomment-304617313, or mute the thread https://github.com/notifications/unsubscribe-auth/AC7u10qtqxvmkeXpX3KTlB4MEBgA9IWwks5r-pBHgaJpZM4NogBK.

ge11232002 commented 7 years ago

There is no JASPAR 2017 yet. I am not sure where you see this.

akhst7 commented 7 years ago

My apologies. When I saw a 2017 core db file (dated 3-16), I thought it was the version updated from the 2016 db.

One quick question. How does TFSBtools compare to DeepBind ?

Thanks.

Aki

On May 30, 2017, at 7:12 AM, Ge Tan notifications@github.com wrote:

There is no JASPAR 2017 yet. I am not sure where you see this.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ge11232002/TFBSTools/issues/11#issuecomment-304846890, or mute the thread https://github.com/notifications/unsubscribe-auth/AC7u14M4QN2w3H9NZF-ohznGYUJF0Xxnks5r-_mMgaJpZM4NogBK.

ge11232002 commented 7 years ago

We didn't systematically compare with DeepBind. TFBSTools stands a conventional way of predicting putative binding sites.