RTN: Reconstruction of transcriptional networks and analysis of master regulators

This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.

AuthorMauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Date of publicationNone
MaintainerMauro Castro <mauro.a.castro@gmail.com>
LicenseArtistic-2.0
Version1.12.0
http://dx.doi.org/10.1038/ncomms3464

View on Bioconductor

Man pages

AVS-class: Class '"AVS"': an S4 class for variant set enrichment...

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.

RTN.data: A pre-processed dataset for the RTN package.

RTN-package: Reconstruction and Analysis of Transcriptional Networks.

TNA-class: Class '"TNA"': an S4 class for Transcriptional Network...

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...

tna.gsea2: Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of...

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.

tni2tna.preprocess: A preprocessing function for objects of class TNI.

tni.bootstrap: Inference of transcriptional networks.

TNI-class: Class '"TNI"': an S4 class for Transcriptional Network...

tni.conditional: Modulators of transcription factor (TF) activity assessed by...

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.

Functions

AVS-class Man page
avs.evse Man page
avs.evse,AVS-method Man page
avs.get Man page
avs.get,AVS-method Man page
avs.plot1 Man page
avs.plot2 Man page
avs.preprocess Man page
avs.preprocess,AVS-method Man page
avs.vse Man page
avs.vse,AVS-method Man page
dt4rtn Man page
RTN Man page
RTN-package Man page
TNA-class Man page
tna.get Man page
tna.get,TNA-method Man page
tna.graph Man page
tna.graph,TNA-method Man page
tna.gsea1 Man page
tna.gsea1,TNA-method Man page
tna.gsea2 Man page
tna.gsea2,TNA-method Man page
tna.mra Man page
tna.mra,TNA-method Man page
tna.overlap Man page
tna.overlap,TNA-method Man page
tna.plot.gsea1 Man page
tna.plot.gsea2 Man page
tna.shadow Man page
tna.shadow,TNA-method Man page
tna.synergy Man page
tna.synergy,TNA-method Man page
tni2tna.preprocess Man page
tni2tna.preprocess,TNI-method Man page
tni.bootstrap Man page
tni.bootstrap,TNI-method Man page
TNI-class Man page
tni.conditional Man page
tni.conditional,TNI-method Man page
tni.dpi.filter Man page
tni.dpi.filter,TNI-method Man page
tni.get Man page
tni.get,TNI-method Man page
tni.graph Man page
tni.graph,TNI-method Man page
tni.permutation Man page
tni.permutation,TNI-method Man page
tni.preprocess Man page
tni.preprocess,TNI-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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