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This functions generates a feature matrix containing 33 network characteristics by differential network analysis.
● Data Source:
CranContrib
● Keywords: network
● Alias: netFeatureMatrix
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The interation-removal method is a gene selection approach based on the removal of interesected interactions in two networks, and has been applied to analyzed the rewiring of genetic interaction maps for identying yeast genes responsive to DNA damage (Bandyopadhyay, et al., 2010; Ideker and Krogan, 2012).
● Data Source:
CranContrib
● Keywords: network
● Alias: interactionRemoval
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This function generates a random seed based on the system time.
● Data Source:
CranContrib
● Keywords: statistic
● Alias: randomSeed
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This function ranks genes based on differential expression analytic method.
● Data Source:
CranContrib
● Keywords: expression
● Alias: geneRanker
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This function extracts the PSOL result.
● Data Source:
CranContrib
● Keywords: PSOL, machine learning
● Alias: PSOL_ResultExtraction
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This function infers transcriptional networks from gene expression data with different statistical methods, including five correlation measures (i.e., the Gini correlation coefficient [GCC], the Pearson's product moment correlation coefficient [PCC], the Kendall tau rank correlation coefficient [KCC], the Spearman's rank correlation coefficient [SCC] and the Tukey's biweight correlation coefficient [BiWt]) and two non-correlation measures (mutual information [MI] and the maximal information-based nonparametric exploration [MINE]).
● Data Source:
CranContrib
● Keywords: network
● Alias: exp2net
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This function selects an initial negative set with the machine learning(ML)-based positive-only sample learning (PSOL) algorithm. The PSOL algorithm has been previously applied to predict genomic loci encoding functional non-coding RNAs (Wang, et al. 2006). We have employed this algorithm to identify stress-related candidate genes in Arabidopsis based on the stress microarray datasets (Ma and Wang, 2013).
● Data Source:
CranContrib
● Keywords: PSOL, machine learning
● Alias: PSOL_InitialNegativeSelection
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This function expands the negative sample set using PSOL algorithm.
● Data Source:
CranContrib
● Keywords: PSOL, machine learning
● Alias: PSOL_NegativeExpansion
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This function generates expression-based features for each gene with the consideration of z-scores, fold changes and actural expression values.
● Data Source:
CranContrib
● Keywords: differential expression
● Alias: expFeatureMatrix
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The ML-based classification model is trained and tested with N-fold cross validation method.
● Data Source:
CranContrib
● Keywords: machine learning
● Alias: cross_validation
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providing 
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