R: Corbi - Collection of Rudimentary Bioinformatics Tools

Corbi-package {Corbi} | R Documentation

## Corbi - Collection of Rudimentary Bioinformatics Tools

### Description

This pakcage provides a bundle of basic and fundamental bioinformatics tools.

### Details

These bioinformatics tools are developed by WuLab at Academy of Mathematics and Systems Science, Chinese Academy of Sciences.

Network querying and alignment:

- `net_query` Network querying method based on conditional random fields

- `net_query_batch` Batch processing version of `net_query`

- `net_align` Network alignment method based on conditional random fields

Subnetwork extraction and search:

- `get_subnets` Enumerate all subnetworks of limited size

- `extend_subnets` Extend subnetworks from smaller subnetworks

- `best_subnets` Search best subnetworks that maximize given objective function

Biomarker identification:

- `markrank` Biomarker identification and prioritization by integrating gene expression with biomolecular network

Differential expression analysis:

- `netDEG` Sample specific differential expression analysis

Data normalization:

- `URG_getFactor` Gene expression data normalization by the uniform ratio graph method

### References

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. An Efficient Network Querying Method Based on Conditional Random Fields. Bioinformatics, 27(22):3173-3178, 2011.

Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. Corbi: A new R package for biological network alignment and querying. BMC Systems Biology, 7(Suppl 2):S6, 2013.

Duanchen Sun, Xianwen Ren, Eszter Ari, Tamas Korcsmaros, Peter Csermely, and Ling-Yun Wu. Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. Briefings in Bioinformatics, 20(1), 89–101, 2019.

Xinhan Ye, Ling-Yun Wu. URG: a new normalization method for gene expression data based on graph model. Manuscript.

[Package Corbi version 0.6-1 Index]