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JEFworks-Lab / HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
http://jef.works/HoneyBADGER/
GNU General Public License v3.0
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example data starting from counts (not scaled or centered) #19

Closed brianjohnhaas closed 5 years ago

brianjohnhaas commented 5 years ago

Hi Jean,

It would be a huge help if you have some example data that start with the raw counts, which could be input through your standard initialization method that then does scaling and centering.

many thanks,

~brian

JEFworks commented 5 years ago

Hi Brian,

Please find linked a Dropbox folder containing the raw data along with a few scripts I used to recreate figures from the original Patel GBM paper back when I was just starting the HoneyBADGER project. There is also a README with additional details.

https://www.dropbox.com/sh/a6xzlk6gujznepf/AADVXV_lMCNI6PoU2DvG3uGna?dl=0

Hope that helps!

Best, Jean

brianjohnhaas commented 5 years ago

Fantastic! Thanks so much!

~brian

On Fri, Jan 25, 2019 at 2:30 PM Jean Fan notifications@github.com wrote:

Hi Brian,

Please find linked a Dropbox folder containing the raw data along with a few scripts I used to recreate figures from the original Patel GBM paper back when I was just starting the HoneyBADGER project. There is also a README with additional details.

https://www.dropbox.com/sh/a6xzlk6gujznepf/AADVXV_lMCNI6PoU2DvG3uGna?dl=0

Hope that helps!

Best, Jean

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JEFworks/HoneyBADGER/issues/19#issuecomment-457696132, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX76kZxjdldfMAIZlq40HZq5gcPC2ks5vG1twgaJpZM4aRfHG .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

myrthesmit commented 3 years ago

Dear Jean,

I had the same question as Brian and tried to access the Dropbox folder you referred to. However, the folder no longer seems to exist. Could you maybe post an updated link to this Dropbox folder?

Thank you very much in advance!

Myrthe