search

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
300 stars 125 forks source link

Error in runJDA "could not find function "runJDA"" #136

Open cynzajac opened 4 years ago

cynzajac commented 4 years ago

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

r3fang commented 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

cynzajac commented 4 years ago

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

r3fang commented 4 years ago

Hi Cynthia,

No problem! Please let me know if you have other question!

cynzajac commented 4 years ago

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!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/136?email_source=notifications&email_token=AIVLBFBKLLSHOGJT4APMBXTQ3645RA5CNFSM4J5MIOAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEICHZPI#issuecomment-570719421, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIVLBFAY7MZAFLSY7XWSMC3Q3645RANCNFSM4J5MIOAA .