New tool: CellNOpt

[aurelien-naldi]

No description provided.

[aurelien-naldi]

Bioconda already has a package for cellnoptr: https://anaconda.org/bioconda/bioconductor-cellnoptr
The CellNopt team also has a python wrapper (using RPy2), for which we probably need a new package.

Including CellNopt (and boolnet) means adding R, it would then make sense to also include R support in the notebooks, as a separate language, not only through rpy2.

[pauleve]

+1 for adding R ; probably in separate branches for now (withR and next-withR), then R/Rpy should probably be moved to colomoto-docker-base when things stabilize

[pauleve]

Given that r-boolnet is now in the image, I guess we can easily include cellnoptr and its rpy2 interface. Is there a conda package for the cellnoptr-rpy2 module?

[aurelien-naldi]

I received an update from Enio Gjerga about a new release and the list of their tools.

These ones are already in the bioconductor channel:

• CellNOptR: bioconductor-cellnoptr 1.32.0
• CNORode: bioconductor-cnorode 1.28.0
• CNORfeeder: bioconductor-cnorfeeder 1.26.0
• CNORdt: bioconductor-cnordt 1.28.0
• CNORfuzzy: bioconductor-cnorfuzzy 1.28.0
• OmnipathR: bioconductor-omnipathr 1.0.0

Only CARNIVAL is still missing but it should appear at some point
https://bioconductor.org/packages/release/bioc/html/CARNIVAL.html

[pauleve]

Great :-) Do they already have some notebooks for demonstration?