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.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.preprocess-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. |
dt4rtn |
A pre-processed dataset for the RTN package. |
RTN |
Reconstruction and Analysis of Transcriptional Networks. |
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.graph |
Compute a graph from TNA objects. |
tna.graph-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.overlap |
Overlap analysis over a list of regulons. |
tna.overlap-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. |
tna.shadow |
shadow analysis over a list of regulons. |
tna.shadow-method |
Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
tna.synergy |
Synergy analysis over a list of regulons. |
tna.synergy-method |
Class '"TNA"': an S4 class for Transcriptional Network Analysis. |
TNI-class |
Class '"TNI"': an S4 class for Transcriptional Network Inference. |
tni.bootstrap |
Inference of 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.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.permutation |
Inference of transcriptional networks. |
tni.permutation-method |
Class '"TNI"': an S4 class for Transcriptional Network Inference. |
tni.preprocess |
A preprocessing function for objects of class TNI. |
tni.preprocess-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. |