C++ implementation of d_edges
Differential Network Analysis Using Gene Pathways
C++ implementation of d_genes
Combine two 'dnapath_list' objects.
Obtain gene symbols for entrezgene IDs
Gene expression dataset for two groups
Get the minimum alpha level for the permutation test
Combine two 'dnapath' objects.
The pathway names in a 'dnapath' object.
Get the two association networks
Plot function for 'dnapath' object.
Remove pathways with non-significant DC scores.
Initialize biomaRt for a given species
Wrapper for GENIE3 method
The number of pathways in a 'dnapath_list' object.
Wrapper for glasso method
Format sepcies name input.
Get the gene names from a differential network analysis
The pathway names in a 'dnapath_list' object.
Wrapper for correlation co-expression
Wrapper for C3Net method
Plot the expression values of two genes
Wrapper for CLR method
Get mean expression of pathway genes in both groups
Internal function for obtaining biomaRt mapping
Wrapper for partial correlations with Empirical Bayes FDR correction
Wrapper for MRNET method
Obtain Reactome pathways
Reactome pathway list for Homo sapiens
Sort function for 'dnapath_list' object.
Rename genes in the differential network analysis
Reverse the order of pathways in a 'dnapath_list' object.
Wrapper for partial correlations from corpcor
Summarize the differential connectivity of pathways.
Return the first part of the dnapath results.
summarize_genes_for_pathway
Summarize differential connectivity of genes in a pathway
Print function for 'dnapath' object.
Wrapper for degree-weighted lasso method
Extract results of a single pathway from a 'dnapath_list' object.
Obtain entrezgene IDs for gene symbols
Return the last part of the dnapath results.
Wrapper for silencer method
Summarize differential connections for a pathway
Extract results of a single pathway from a 'dnapath' object.
Summarize the differential connectivity of genes over all pathways.
Replace parts of a 'dnapath' object.
Subset function for 'dnapath_list' object.
Replace parts of a 'dnapath_list' object.
Print function for 'dnapath_list' object.
Wrapper for ARACNE method
Summary function for 'dnapath_list' object.
Summary function for 'dnapath' object.
Wrapper for BC3Net method
Extract results of a single pathway from a 'dnapath' object.
Extract parts of a 'dnapath_list' object.
Default mapping for entrezgene IDs and HGNC gene symbols
combine_overlapping_pathways
Modify a pathway list to combine overlapping pathways.
C++ implementation of d_pathway
A short title line describing what the package does
Differential network analysis on a single pathway