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

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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.

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

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