Package: RTN 2.37.0

Mauro Castro

RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

Authors:Clarice Groeneveld [ctb], Gordon Robertson [ctb], Xin Wang [aut], Michael Fletcher [aut], Florian Markowetz [aut], Kerstin Meyer [aut], and Mauro Castro [aut]

RTN_2.37.0.tar.gz
RTN_2.37.0.zip(r-4.7)RTN_2.37.0.zip(r-4.6)RTN_2.37.0.zip(r-4.5)
RTN_2.37.0.tgz(r-4.6-any)RTN_2.37.0.tgz(r-4.5-any)
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RTN_2.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTN/json (API)

# Install 'RTN' in R:

install.packages('RTN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pksData - Pre-processed datasets for the RTN package.
stni - A pre-processed TNI for demonstration purposes only.
tfsData - Pre-processed datasets for the RTN package.
tnaData - Pre-processed datasets for the RTN package.
tniData - Pre-processed datasets for the RTN package.

On BioConductor:RTN-2.37.0(bioc 3.24)RTN-2.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

transcription network networkinference networkenrichment generegulation geneexpression graphandnetwork genesetenrichment geneticvariability

6.16 score 2 packages 80 scripts 17 mentions 36 exports 133 dependencies

Last updated from:8d8eb9db75. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	190
linux-devel-x86_64	NOTE	388
source / vignettes	OK	346
linux-release-x86_64	NOTE	385
macos-release-arm64	NOTE	236
macos-oldrel-arm64	NOTE	226
windows-devel	NOTE	291
windows-release	NOTE	269
windows-oldrel	NOTE	275
wasm-release	OK	173

Exports:avs.evse avs.get avs.pevse avs.plot1 avs.plot2 avs.rvse avs.vse tna.get tna.gsea1 tna.gsea2 tna.mra tna.plot.gsea1 tna.plot.gsea2 tni.alpha.adjust tni.annotate.regulons tni.annotate.samples tni.area3 tni.bootstrap tni.conditional tni.constructor tni.dpi.filter tni.get tni.graph tni.gsea2 tni.overlap.genesets tni.permutation tni.plot.checks tni.plot.sre tni.preprocess tni.prune tni.regulon.summary tni.replace.samples tni.sre tni2tna.preprocess upgradeTNA upgradeTNI

Dependencies:abind askpass backports base64enc Biobase BiocGenerics boot broom bslib cachem car carData class cli colorspace cowplot cpp11 crosstalk curl data.table DelayedArray Deriv digest doBy dplyr e1071 evaluate farver fastmap fontawesome forecast Formula fracdiff fs generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph infotheo IRanges isoband jquerylib jsonlite kernlab KernSmooth knitr labeling later lattice lazyeval lifecycle limma lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minet minqa mixtools modelr nlme nloptr nnet numDeriv openssl otel pbkrtest pheatmap pillar pkgconfig plotly promises proxy purrr pwr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack RedeR reformulas rlang rmarkdown S4Arrays S4Vectors S7 sass scales segmented Seqinfo snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viper viridisLite withr xfun XVector yaml zoo

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons.

Rendered fromRTN.Rmdusingknitr::rmarkdown

Last update: 2023-11-23
Started: 2017-09-29

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

Package: RTN 2.37.0

RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

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