## ----message=FALSE, warning=FALSE---------------------------------------------------------------------------
library(OmnipathR)

## ----chalmers-raw-------------------------------------------------------------------------------------------
ch_raw <- chalmers_gem_raw()

## ----chalmers-proc------------------------------------------------------------------------------------------
ch_processed <- chalmers_gem()
names(ch_processed)

## ----chalmers-id--------------------------------------------------------------------------------------------
ch_met <- chalmers_gem_metabolites()

ch_met

## ----chalmers-idtrans, eval = FALSE-------------------------------------------------------------------------
# translate_ids('MAM00001', 'metabolicatlas', 'recon3d', chalmers = TRUE)

## ----chalmers, eval = FALSE---------------------------------------------------------------------------------
# ch <- chalmers_gem_network()
# 
# ch

## ----stitch-actions, eval = FALSE---------------------------------------------------------------------------
# sta <- stitch_actions()
# 
# sta

## ----stitch-links, eval = FALSE-----------------------------------------------------------------------------
# stl <- stitch_links()
# 
# stl

## ----stitch, eval = FALSE-----------------------------------------------------------------------------------
# st <- stitch_network()
# 
# st

## ----omnipath-----------------------------------------------------------------------------------------------
op <- omnipath_for_cosmos()

op

## ----cosmos, eval = FALSE-----------------------------------------------------------------------------------
# pkn <- cosmos_pkn()
# 
# pkn

## ----session------------------------------------------------------------------------------------------------
sessionInfo()