AVS-class               Class '"AVS"': an S4 class for variant set
                        enrichment analysis.
RTN-package             Reconstruction and Analysis of Transcriptional
                        Networks.
TNA-class               Class '"TNA"': an S4 class for Transcriptional
                        Network Analysis.
TNI-class               Class '"TNI"': an S4 class for Transcriptional
                        Network Inference.
avs.evse                An eQTL/VSE pipeline for variant set enrichment
                        analysis.
avs.get                 Get information from individual slots in an AVS
                        object.
avs.plot1               Plot results from AVS methods, single plots.
avs.plot2               Plot results from AVS methods, multiple plots.
avs.preprocess          A preprocessing function for objects of class
                        AVS.
avs.vse                 Variant set enrichment (VSE) analysis.
dt4rtn                  A pre-processed dataset for the RTN package.
tna.get                 Get information from individual slots in a TNA
                        object.
tna.graph               Compute a graph from TNA objects.
tna.gsea1               One-tailed Gene Set Enrichment Analysis (GSEA)
                        over a list of regulons.
tna.gsea2               Two-tailed Gene Set Enrichment Analysis (GSEA)
                        over a list of regulons.
tna.mra                 Master Regulator Analysis (MRA) over a list of
                        regulons.
tna.overlap             Overlap analysis over a list of regulons.
tna.plot.gsea1          Plot enrichment analyses from TNA objects.
tna.plot.gsea2          Plot enrichment analyses from TNA objects.
tna.shadow              shadow analysis over a list of regulons.
tna.synergy             Synergy analysis over a list of regulons.
tni.bootstrap           Inference of transcriptional networks.
tni.conditional         Modulators of transcription factor (TF)
                        activity assessed by conditional mutual
                        information analysis.
tni.dpi.filter          Data Processing Inequality (DPI) filter.
tni.get                 Get information from individual slots in a TNI
                        object.
tni.graph               Compute a graph from TNI objects.
tni.permutation         Inference of transcriptional networks.
tni.preprocess          A preprocessing function for objects of class
                        TNI.
tni2tna.preprocess      A preprocessing function for objects of class
                        TNI.
