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.pevse               An EVSE pipeline using precomputed eQTLs.
avs.plot1               Plot results from AVS methods, single plots.
avs.plot2               Plot results from AVS methods, multiple plots.
avs.vse                 Variant set enrichment (VSE) analysis.
stni                    A pre-processed TNI for demonstration purposes
                        only.
tna.get                 Get information from individual slots in a TNA
                        object.
tna.graph               Compute a graph from TNA objects (deprecated
                        function).
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
                        (deprecated function).
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
                        (deprecated function).
tna.synergy             Synergy analysis over a list of regulons
                        (deprecated function).
tni.area3               Compute regulon activity by calling aREA
                        (analytic Rank-based Enrichment Analysis)
                        algorithm
tni.bootstrap           Inference of consensus transcriptional
                        networks.
tni.conditional         Modulators of transcription factor (TF)
                        activity assessed by conditional mutual
                        information analysis.
tni.constructor         A constructor for objects of class TNI.
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.gsea2               Compute regulon activity by calling GSEA2
                        (two-tailed Gene Set Enrichment Analysis)
                        algorithm
tni.permutation         Inference of transcriptional networks.
tni.preprocess          A preprocessing function for objects of class
                        TNI.
tni.prune               Prune regulons to remove redundant targets for
                        regulon activity analysis
tni.regulon.summary     Summary of regulon characteristics
tni.replace.samples     Entry point to assess new samples with
                        previously calculated regulons.
tni2tna.preprocess      A preprocessing function for objects of class
                        TNI.
tniData                 Pre-processed datasets for the RTN package.
upgradeTNA              Upgrade objects of class TNI.
upgradeTNI              Upgrade objects of class TNI.
