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SPADE script to install package in R

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fcl54643

Contributor

Posts: 21

Joined: Mon Nov 02, 2015 2:13 pm

Location: Greater Philadelphia Area

Post Tue Feb 12, 2019 9:32 pm

SPADE script to install package in R

I would like to install the SPADE package on R, however I am not able to do so using BiocManager. Below is the script I used and error message that followed:

BiocManager ::install("spade")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'spade'
installation path not writeable, unable to update packages: class, codetools,
mgcv

My understanding is that SPADE has been removed from Bioconductor, hence the script above did not result in successful installation.

Would any of you know whether it is still possible to install SPADE in R, and if so, could you suggest a script? We are moving away from SPADE in favor of FlowSOM, however we might still want to run a SPADE analysis once in a while.

Thank you,

Florence
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Feb 13, 2019 4:12 pm

Re: SPADE script to install package in R

Hi Florence,

It looks like the *tar.gz is still available here: https://www.bioconductor.org/packages/3 ... spade.html

Alternatively, Peng Qiu has a MATLAB-implementation: http://pengqiu.gatech.edu/software/SPADE/


Mike
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Wed Feb 13, 2019 4:24 pm

Re: SPADE script to install package in R

Out of curiosity, may I ask why you are looking to use SPADE? Both FlowSOM and Phenograph mostly replaced it as a clustering tool.
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fcl54643

Contributor

Posts: 21

Joined: Mon Nov 02, 2015 2:13 pm

Location: Greater Philadelphia Area

Post Thu Feb 14, 2019 5:41 pm

Re: SPADE script to install package in R

Thank you, Mike! Looks like MATLAB would be the only option (the new version of R does not seem to support SPADE). We were hoping to install the package on R to have the flexibility to run SPADE analysis in FlowJo. Not a big deal since we will mostly be using FlowSOM as a clustering tool for now. Thank you again.

Florence
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Feb 14, 2019 5:50 pm

Re: SPADE script to install package in R

HI Florence,

It looks like SPADE is also built into Cytosplore: https://www.cytosplore.org/documentatio ... onoverview


Regarding R: If you download the *tar.gz, then you can go into RStudio:
Packages
Install
Install from Package Archive File (rather than CRAN)


I just tried that installation, and it worked for me.

Mike

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