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| RTN-package | Reconstruction and Analysis of Transcriptional Networks. |
| AVS-class | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| avs.evse | An eQTL/VSE pipeline for variant set enrichment analysis. |
| avs.evse-method | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| avs.get | Get information from individual slots in an AVS object. |
| avs.get-method | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| avs.pevse | An EVSE pipeline using precomputed eQTLs. |
| avs.pevse-method | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| avs.plot1 | Plot results from AVS methods, single plots. |
| avs.plot2 | Plot results from AVS methods, multiple plots. |
| avs.rvse | An rQTL/VSE pipeline for variant set enrichment analysis. |
| avs.rvse-method | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| avs.vse | Variant set enrichment (VSE) analysis. |
| avs.vse-method | Class '"AVS"': an S4 class for variant set enrichment analysis. |
| pksData | Pre-processed datasets for the RTN package. |
| RTN | Reconstruction and Analysis of Transcriptional Networks. |
| stni | A pre-processed TNI for demonstration purposes only. |
| tfsData | Pre-processed datasets for the RTN package. |
| TNA-class | Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
| tna.get | Get information from individual slots in a TNA object. |
| tna.get-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
| tna.gsea1 | One-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons. |
| tna.gsea1-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
| tna.gsea2 | Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons. |
| tna.gsea2-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
| tna.mra | Master Regulator Analysis (MRA) over a list of regulons. |
| tna.mra-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
| tna.plot.gsea1 | Plot enrichment analyses from TNA objects. |
| tna.plot.gsea2 | Plot enrichment analyses from TNA objects. |
| tnaData | Pre-processed datasets for the RTN package. |
| TNI-class | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.alpha.adjust | Adjust the significance level for two datasets. |
| tni.annotate.regulons | Annotate regulons with external gene set collections. |
| tni.annotate.regulons-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.annotate.samples | Annotate samples with external gene set collections. |
| tni.annotate.samples-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.area3 | Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm |
| tni.area3-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.bootstrap | Inference of consensus transcriptional networks. |
| tni.bootstrap-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.conditional | Modulators of transcription factor (TF) activity assessed by conditional mutual information analysis. |
| tni.conditional-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.constructor | A constructor for objects of class TNI. |
| tni.dpi.filter | Data Processing Inequality (DPI) filter. |
| tni.dpi.filter-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.get | Get information from individual slots in a TNI object. |
| tni.get-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.graph | Compute a graph from TNI objects. |
| tni.graph-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.gsea2 | Compute regulon activity by calling GSEA2 (two-tailed Gene Set Enrichment Analysis) algorithm |
| tni.gsea2-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.overlap.genesets | Associate regulons with external gene set collections. |
| tni.overlap.genesets-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.permutation | Inference of transcriptional networks. |
| tni.permutation-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| 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.preprocess-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.prune | Prune regulons to remove redundant targets for regulon activity analysis |
| tni.prune-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.regulon.summary | Summary of regulon characteristics. |
| tni.regulon.summary-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.replace.samples | Entry point to assess new samples with previously calculated regulons. |
| tni.replace.samples-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni.sre | Subgroup Regulon Enrichment for TNI-class objects. |
| tni.sre-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tni2tna.preprocess | A preprocessing function for objects of class TNI. |
| tni2tna.preprocess-method | Class '"TNI"': an S4 class for Transcriptional Network Inference. |
| tniData | Pre-processed datasets for the RTN package. |
| upgradeTNA | Upgrade objects of class TNI. |
| upgradeTNI | Upgrade objects of class TNI. |