README.md

SCoR - An R package for Microbiome Correlation

Installation

library(devtools)
devtools:install_github("AbhishakeL/SCoR")

Pre-requisites

Install FastSpar.

Pipeline

1. Create a phyloseq object. Possible examples can be found here or here .
2. Use FSprep() to create metadata attribute-wise partitioned OTU table.
3. Write the output of the previous command to a file.
4. Run FastSpar on the previous file.

5. Remove the # from the first cell in the correlation table and p-value table output from FastSpar.

6. Use scor() to generate the final output. Please follow example for details of parameter.
7. Visualise network using igraph or Cytoscape.

Flowchart

flowchart TD
    A[/phyloseq object/] --> B[FSprep]
    B --> C[/Filtered OTU table/]
    C --> D[FastSpar]
    D --> E[/Correlation matrix & p-value matrix/]
    E --> F[scor]
    C --> F
    F --> G[igraph object]
    F --> H[Correlation threshold values]
    F --> I[Final correlation matrix]

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