Requirements

Manual installation of package requirements

The following packages are required for transcriptomic data integration, parameter estimation, patient-specific simulations, and result visualization.

General:

• Python >= 3.7
• Julia >= 1.5
• R >= 4.0

Python:

$ pip install -r requirements.txt

• pasmopy==0.1.0
• biomass>=0.5.2,<0.6
• matplotlib==3.3.4
• numpy==1.19.2
• pandas==1.2.4
• seaborn==0.11.2
• scipy==1.6.0

Julia:

$ julia
julia> ] add BioMASS @0.5.0

• BioMASS.jl==0.5.0

R:

$ R
> source("install_requirements.R")

• TCGAbiolinks
• sva
• biomaRt
• ComplexHeatmap
• viridisLite
• dplyr
• edgeR
• tibble
• data.table
• stringr