Identification of upstream transcription factors for all genes.
Find overlap of next neighbors of transcription factors in identified
pathways.
Get genes intersection for the omics data on the different time points.
Map alias names to STRING IDs of consensus graph.
Generate genelists from pathway databases.
Get all gene IDs.
Generate internally genelists from pathway databases.
Identification of upstream transcription factors.
Get TF intersection for the omics data on the different time points.
Steiner tree algorithm.
Prepare OmicsData object for pathway information.
Get upstream regulators of identified transcription factors.
Get upstream regulators of identified transcription factors.
Get upstream TFs.
Identification of pathwayIDs and pathway names for proteins at individual
timepoints.
Get upstream pathways of identified transcription factors.
Transcription factor enrichment - upstream analysis.
Get all protein IDs.
Plot consensus graph profiles of static consensus molecules.
Find next neighbors of transcription factors in identified pathways.
Internal subfunction for all protein pathway identification.
Get protein intersection for the omics data on the different time points.
Identify pathway IDs and pathway names of differentially abundant proteins
Prepare OmicsData object for pathway information.
Get consensus graph in STRING IDs.
Add feedback loops from target genes to proteins/TFs if present.
Get downstream analysis target genes of TFs found in pathways.
Read in omics data.
Get omics data intersection on the three levels.
Identification of pathways containing the transcription factors identified in
upstream analysis
Get TF-target gene information for the consensus graph.
Get Gene Symbols from Ensemble Gene Accession IDs.
Generate STRING PPI graph.
Plot time profile clusters of dynamic analysis result.
Transcription factor identification.
Plot inferred net based on analysis analysis.
Read in matching transcription factor target gene pairs.
Identify TFs in enriched pathways and their target genes - downstream
analysis.
Reads in chosen transcription factor target database information.
Clustering of time profiles.
Combine SteinerNet with bipartite graph to get full consensus network.
Get Omics dataset.
Get Omics timepoints.
Read in pathway database data needed for pathway identification.
Static analysis.
Get downstream analysis transcription factors in pathways.
Print an OmicsData object.
Create internal IDs.
Get fold change splines.
Plot consensus graph(s) from static analysis.
Identify regulators of enriched transcription factors - upstream analysis.
Pathway-based data integration of omics data
Select pathways with more than x TFs
Loading of genelists
Create a new Biopax model containing all database information.
Dynamic analysis.
Internal function for generation of pathway database specific internal IDs.
Identification of pathwayIDs and pathway names for all proteins.
Omics example dataset.
Pathway enrichment - downstream analysis.
Get downstream analysis pathways.
This function provides a data.table of upstream transcription factors and the
flag for enrichment.
Load pathway database information.
Prediction of continous data points via smoothing splines.
Identify overlapping upstream regulators of x transcription factors