Open cynzajac opened 4 years ago
Hi Cynthia,
The latest version of SnapATAC disables "runJDA" function. Instead, I have replaced it with another function called "runDiffusionMaps". Please take a look in example 1. The new dimensionality reduction technique is more robust to read depth bias and easier to scale up to large dataset.
https://github.com/r3fang/SnapATAC/blob/master/examples/10X_brain_5k/README.md
Hi Rong,
Thanks so much for getting back. Yes, I will try that.
Best, Cynthia
Sent from my iPad
On Jan 2, 2020, at 6:09 PM, Rongxin Fang notifications@github.com wrote:
Hi Cynthia,
The latest version of SnapATAC disables "runJDA" function. Instead, I have replaced it with another function called "runDiffusionMaps". Please take a look in example 1. The new dimensionality reduction technique is more robust to read depth bias and easier to scale up to large dataset.
https://github.com/r3fang/SnapATAC/blob/master/examples/10X_brain_5k/README.md
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Hi Cynthia,
No problem! Please let me know if you have other question!
Hi Rong,
Will do.
Thanks, Cynthia
On Fri, Jan 3, 2020 at 5:38 PM Rongxin Fang notifications@github.com wrote:
Hi Cynthia,
No problem! Please let me know if you have other question!
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Hi,
I am having trouble running the function "runJDA". I was looking at the man, and pretty much searching everywhere in your repo and online, but I haven't found a solution. Was this function discontinued on the last "SnapATAC" update? Thats the one I am currently running
Thank you! Cynthia