Installation

[genignored]

Just a quick FYI.

As installing SAFEclustering into a fresh directory (pointing R_LIBS_USER to a clean directory, to make sure I don't overwrite other stuff), I am unable to run

devtools::install_github("yycunc/SAFEclustering")

as it fails on the 'cidr' requirement.

I was able to work around by installing it separately, but it may not be as easy for others.

devtools::install_github("VCCRI/CIDR")

also not certain that's the correct version of cidr

[yycunc]

Hi,

Thanks for interesting in our method. Both SAFE and SAMEclustering implement cluster ensemble on four individual solutions from SC3, CIDE, Seurat and t-SNE + kmeans, although they can also work on the results of different combinations as well as from other scRNA-seq clustering methods. Since our default is to do consensus clustering on all the four methods, our packages require the package of each method to be first installed into R. However, as there are more and more newly developed scRNA-seq clustering, it is not necessary to use these four methods for SAFE/SAMEclustering. Users can first perform clustering by themselves using the desired clustering method and then using the results as the input for the cluster ensemble.

I will update the package recently, which will not require users to install the packages for each individual methods any more. I hope that will give users more flexibility.

Thanks for your good suggestion.

[adiko-junior]

Salut,

J'espere que vous allez bien?
Svp j'ai un problemed lors de l'installation du package SAFEclustering.
J'obtient une erreur obligeant le package "cidr".

Mais l'installation a l'aide de commande devtools::install_github("VCCRI/CIDR") me retourne
"had non-zero exit status " comme erreur. Avez-vous une idée de comment je pourrai le resoudre?

Merci cordialement.

[yycunc]

Hi, Thanks for interested in our method. Actually I don't know any French, so please don't mind that I reply this email in English. CIDR is a method published in almost 5 years ago and the authors haven't updated it since that. Its speed is slow and not suitable for large datasets. So now it is not a good method to incorporate in clustering ensemble. It is better now to not install CIDR at all and set the argument CIDR = FALSE to disable CIDR and only use the other three methods. I hope it helps and please feel free to let me know if you have any other questions. Bests, Yuchen

…

--- Yuchen Yang, Ph.D. School of Ecology Sun Yat-sen University Xingangxi Road 135, Guangzhou 510275, China Email: ***@***.*** adiko-junior ***@***.***> 于2022年2月17日周四 06:51写道：

Salut, J'espere que vous allez bien? Svp j'ai un problemed lors de l'installation du package SAFEclustering. J'obtient une erreur obligeant le package "cidr". Mais l'installation a l'aide de commande devtools::install_github("VCCRI/CIDR") me retourne "had non-zero exit status " comme erreur. Avez-vous une idée de comment je pourrai le resoudre? Merci cordialement. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJPXJ6JULCT3RYJSICFTN2DU3QS57ANCNFSM4KX54LFA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>