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Rbims Logo Rbims

R tools for reconstructing bin metabolisms.

Quick install

We are actively developing rbims, for now it is not available at CRAN or Bioconductor, however you can access the development version from GitHub.

In R terminal:

install.packages("devtools")

If you are in a MAC system, you will need to download XQuartz, you can read more about it here. As well if you are in ubuntu you need to install libcairo2-dev, you can read more about it here.

library(devtools)
install_github("mirnavazquez/RbiMs")
library(rbims)

Overview

Logo Rbims 3

Visit the website for more detail.

New function to write a metabolism workbook

If you want to create a metabolism table in excel that includes KEGG and interproscan outputs you can use this new function.

library(rbims)
write_metabolism("Interpro_test.tsv", 
                 "path/to/KEGG/output/")

Contributions

  • Mirna Vázquez Rosas Landa - wrote the code.
  • Karla López - wrote codes and manuscript, helped with documentation.
  • Stephanie Hereira - Helped with functions and documentation.
  • Diana Oaxaca - Set the conda environment.
  • Frida Ruiz - Heleped with testing and documentation.

References

  • Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).
  • Kanehisa, M; Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28, 1947-1951 (2019).
  • Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M., and Tanabe, M.; KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 49, D545-D551 (2021).
  • DiTing cycles definition.