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Online availability of Cytofast

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Jessica

Participant

Posts: 2

Joined: Mon Dec 18, 2017 9:27 pm

Post Fri Nov 23, 2018 2:55 pm

Online availability of Cytofast

I recently read the paper "Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations", by Beyrend et al. 2018 in Computational and Structural Biotechnology. The authors claim that their R code is available as a package in Bioconductor, but I can find no such package on the Bioconductor website.

Has anyone been able to use it?

Thanks
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Sat Nov 24, 2018 6:39 pm

Re: Online availability of Cytofast

Hi,
The package is not yet available at Bioconductor.
It is available at github https://github.com/KoenAStam/cytofast
You can try to install from github. If you are already on bioconductor v3.8, use the lazy/easy command BiocManager::install("KoenAStam/cytofast")
Happy HSNE & cytofast ;-)
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Jessica

Participant

Posts: 2

Joined: Mon Dec 18, 2017 9:27 pm

Post Mon Nov 26, 2018 2:56 pm

Re: Online availability of Cytofast

I get this error message:

Error: package 'remotes' not installed in library path(s)
/Library/Frameworks/R.framework/Versions/3.5/Resources/library
install with 'install("remotes")'

I tried to install package 'remotes', but I can't get it to install.

Is there a way I can install it from GitHub? I understand I could download the files, but I don't know how to install it from there.

Thanks
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sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Mon Nov 26, 2018 3:16 pm

Re: Online availability of Cytofast

Try to install remotes packages from CRAN using install.packages("remotes").
Then redo your command to install cytofast.
If it fails again, please post the command you entered,
or start an issue at https://github.com/KoenAStam/cytofast/issues
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gbeyrend

Participant

Posts: 2

Joined: Mon Nov 26, 2018 12:18 pm

Post Tue Nov 27, 2018 7:30 am

Re: Online availability of Cytofast

Dear all,
thank you for using our tool Cytofast.
The answer of sgrandjeaud is already very complete. Our package is already available in Github as written in the paper. You can install it with the vignette by the R command line:
  Code:
BiocManager::install("KoenAStam/cytofast", build_vignettes=T)


We are preparing a new version for Bioconductor with more details, with new statistical tests and a tutorial video. You will be notified as soon as it is made available.
Enjoy HSNE & Cytofast
Best,

Guillaume Beyrend

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