TODO.md

In gongcongcong/mbOmic: Integrative analysis of the microbiome and metabolome

TODO LIST:

• add enterotype to the network of metabolites and OTU

• add food/diet module and link it to the gut OTU and gut microbiota metabolites module;

  ref: Noronha, A., Modamio, J., Jarosz, Y., Guerard, E., Sompairac, N., Preciat, G., ... & Thiele, I. (2019). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic acids research, 47(D1), D614-D624.

  website: Virtual Metabolic Human (vmh.life)

• Establish three modules and their relationship: gut microbiota (OTU); gut microbiota metabolites; food/diet;

API:

1. microbe
2. metabolites
3. gene
4. food items

class:

vmh:

1. type (character): microbe, metabolites, gene, food items

2. net (data.table):

   • microbe
   • metabolites
   • gene
   • food items
   • reaction

methods

corr:

1. mSet, bSet
2. network

?

gongcongcong/mbOmic documentation built on July 1, 2023, 1:47 p.m.