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.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.plot.gsea1          Plot enrichment analyses from TNA objects.
tna.plot.gsea2          Plot enrichment analyses from TNA objects.
tni.alpha.adjust        Adjust the significance level for two datasets.
tni.annotate.regulons   Annotate regulons with external gene set
                        collections.
tni.annotate.samples    Annotate samples with external gene set
                        collections.
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.overlap.genesets    Associate regulons with external gene set
                        collections.
tni.permutation         Inference of transcriptional networks.
tni.plot.checks         Plot regulon target counts.
tni.plot.sre            Plot Subgroup Regulon Enrichment for TNI-class
                        objects.
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.
tni.sre                 Subgroup Regulon Enrichment for TNI-class
                        objects.
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.
