RTN: Reconstruction of transcriptional networks and analysis of master regulators

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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.

Author
Mauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Date of publication
None
Maintainer
Mauro Castro <mauro.a.castro@gmail.com>
License
Artistic-2.0
Version
1.12.0
URLs

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.

Files in this package

RTN/DESCRIPTION
RTN/NAMESPACE
RTN/R
RTN/R/AVS-methods.R
RTN/R/AllChecks.R
RTN/R/AllClasses.R
RTN/R/AllGenerics.R
RTN/R/AllPlotsAVS.R
RTN/R/AllPlotsTNA.R
RTN/R/AllSupplementsAVS.R
RTN/R/AllSupplementsTNA.R
RTN/R/AllSupplementsTNI.R
RTN/R/ClassUnions.R
RTN/R/TNA-methods.R
RTN/R/TNI-methods.R
RTN/build
RTN/build/vignette.rds
RTN/data
RTN/data/datalist
RTN/data/dt4rtn.RData
RTN/inst
RTN/inst/CITATION
RTN/inst/NEWS.Rd
RTN/inst/doc
RTN/inst/doc/RTN.R
RTN/inst/doc/RTN.Rnw
RTN/inst/doc/RTN.pdf
RTN/inst/unitTests
RTN/inst/unitTests/test.R
RTN/man
RTN/man/AVS-class.Rd
RTN/man/RTN-package.Rd
RTN/man/RTN.data.Rd
RTN/man/TNA-class.Rd
RTN/man/TNI-class.Rd
RTN/man/avs.evse.Rd
RTN/man/avs.get.Rd
RTN/man/avs.plot1.Rd
RTN/man/avs.plot2.Rd
RTN/man/avs.preprocess.Rd
RTN/man/avs.vse.Rd
RTN/man/tna.get.Rd
RTN/man/tna.graph.Rd
RTN/man/tna.gsea1.Rd
RTN/man/tna.gsea2.Rd
RTN/man/tna.mra.Rd
RTN/man/tna.overlap.Rd
RTN/man/tna.plot.gsea1.Rd
RTN/man/tna.plot.gsea2.Rd
RTN/man/tna.shadow.Rd
RTN/man/tna.synergy.Rd
RTN/man/tni.bootstrap.Rd
RTN/man/tni.conditional.Rd
RTN/man/tni.dpi.filter.Rd
RTN/man/tni.get.Rd
RTN/man/tni.graph.Rd
RTN/man/tni.permutation.Rd
RTN/man/tni.preprocess.Rd
RTN/man/tni2tna.preprocess.Rd
RTN/tests
RTN/tests/runTests.R
RTN/vignettes
RTN/vignettes/RTN.Rnw
RTN/vignettes/bib.bib