saezverse

Docker image with all tools from the Saez lab based on bioconductor/bioconductor_docker.

To run a container locally use the command:

docker run -p 8787:8787 tanevski/saezverse:latest

This will make RStudio available at http://localhost:8787. Login with username rstudio and password saezlab.

R packages

Package	More info
BiRewire	https://bioconductor.org/packages/BiRewire
CARNIVAL	https://bioconductor.org/packages/CARNIVAL
CellNOptR	https://www.bioconductor.org/packages/CellNOptR
CNORdt	https://www.bioconductor.org/packages/CNORdt
CNORfeeder	https://www.bioconductor.org/packages/CNORfeeder
CNORfuzzy	https://www.bioconductor.org/packages/CNORfuzzy
CNORode	https://www.bioconductor.org/packages/CNORode
cosmosR	https://www.bioconductor.org/packages/cosmosR
decoupleR	https://www.bioconductor.org/packages/decoupleR
dorothea	https://www.bioconductor.org/packages/dorothea
LIANA	https://github.com/saezlab/liana
mistyR	https://www.bioconductor.org/packages/mistyR
ocean	https://github.com/saezlab/ocean
OmnipathR	https://www.bioconductor.org/packages/OmnipathR
PHONEMeS	https://github.com/saezlab/PHONEMeS-ILP
progeny	https://www.bioconductor.org/packages/progeny
SLAPenrich	https://github.com/saezlab/SLAPenrich
wppi	https://www.bioconductor.org/packages/wppi

Python packages

Package	More info
decoupler	https://pypi.org/project/decoupler/
kinact	https://github.com/saezlab/kinact
omnipath	https://pypi.org/project/omnipath/
pypath	https://pypi.org/project/pypath-omnipath/