Corbi-package {Corbi}

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.