This pakcage provides a bundle of basic and fundamental bioinformatics tools.
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
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<U+2013>101, 2019.
Xinhan Ye, Ling-Yun Wu. URG: a new normalization method for gene expression data based on graph model. Manuscript.