csdR {csdR} | R Documentation

## Perform differential co-expression analysis

### Description

This package provides functionality to perform differential co-expression analysis by the CSD algorithm presented by Voigt et al. 2017. The main function of the package is `run_csd` which compares gene expression for two conditions and returns values for C, S and D for each gene pair. Also, the underlying function `run_cor_bootstrap` is provided for doing correlation analysis within a condition, but is mostly for experimental and expect use only.

The function `partial_argsort` is aimed specifically at the task of selecting the highest values of C, S and D of the results with minimal computational overhead, but is written also to be useable for other problems of the same type.

For more details on how to approach, please read the vignette for the package or the individual manpages for the functions.

### Author(s)

Maintainer: Jakob Peder Pettersen jakobpeder.pettersen@gmail.com (ORCID)

### References

Voigt A, Nowick K and Almaas E 'A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma' In: PLOS Computational Biology 13(9): e1005739. (doi: https://doi.org/10.1371/journal.pcbi.1005739)

### See Also

Useful links:

- https://almaaslab.github.io/csdR

- https://github.com/AlmaasLab/csdR

- Report bugs at https://github.com/AlmaasLab/csdR/issues

[Package csdR version 1.0.0 Index]