/inteSIN

integrated sample-specific inference networks

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

Contributors

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.