rusher321/intesin

integrated sample-specific inference networks

inteSIN: integrate sample-specific inference network methods. This package now includes SSN, LIONESS, SSPGI, iENA, CSN and Sweet. The flowchart is below.

Contributors

• Huahui Ren
• Mingyue Zhao

Comments and contributions

Installation

This package can be installed using devtools.

devtools::install_github('rusher321/inteSIN')

We welcome comments, criticisms, and especially contributions! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here:

https://github.com/rusher321/inteSIN/issues

🥶 TODO

• DNB function

• network visualization

• degree matrix visualization

• other SIN methods test on microbiome datasets (CRC; Antibiotic; Infant...)

  • collect 3 CRC cohorts/1 antibiotic/ 1 longitudinal infant (bacteria or virome) cohort and preprocess.
    • the metaphlan3 profiling (XXX et al., XXX et al., ...) from curatedMetagenomicData.
    • 🦊low priority:the virome profiling of infants could be generated using Phanta , the data is in here.
  • comparison between biomarkers based on expression data and degree data.
  • performance of classification, one option is Stabl, which could integrate the degree matrix and expression matrix using the data fusion.
  • antibiotic: Which specific sample networks have higher antibiotic resistance
  • infant: the change of specific sample network during the early life
  • A gut microbial signature for combination immune checkpoint blockade across cancer types

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for inteSIN in R doing citation(package = 'inteSIN')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.