Package: RegEnrich 1.17.0

Weiyang Tao

RegEnrich: Gene regulator enrichment analysis

This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.

Authors:Weiyang Tao [cre, aut], Aridaman Pandit [aut]

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RegEnrich.pdf |RegEnrich.html✨
RegEnrich/json (API)
NEWS

# Install 'RegEnrich' in R:

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

Datasets:

Lyme_GSE63085 - Example RNAseq dataset [Human]
TFs - Human gene regulators

On BioConductor:RegEnrich-1.17.0(bioc 3.21)RegEnrich-1.16.0(bioc 3.20)

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

geneexpression transcriptomics rnaseq twochannel transcription genetarget networkenrichment differentialexpression network networkinference genesetenrichment functionalprediction

3.94 score 22 scripts 194 downloads 1 mentions 23 exports 147 dependencies

Last updated 23 days agofrom:231e44e051. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:%>%getResultsNames head newDeaSet newScore newTopNetwork plot_Enrich plotOrders plotRegTarExpr plotSoftPower regenrich_diffExpr regenrich_enrich regenrich_network regenrich_network<-regenrich_rankScore RegenrichSet results_DEA results_enrich results_expr results_score results_topNet show tail

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocManager BiocParallel BiocSet BiocStyle Biostrings bit bit64 blob bookdown bslib cachem checkmate cli cluster codetools colorspace cowplot cpp11 crayon curl data.table DBI DelayedArray DESeq2 digest doParallel DOSE dplyr dynamicTreeCut evaluate fansi farver fastcluster fastmap fastmatch fgsea fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue GO.db GOSemSim gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet ontologyIndex openssl pillar pkgconfig plogr plyr png preprocessCore purrr qvalue R.methodsS3 R.oo R.utils R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang rmarkdown rpart RSQLite rstudioapi S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite WGCNA withr xfun XVector yaml yulab.utils zlibbioc

RegEnrich: an R package for gene regulator enrichment analysis

Weiyang Tao, Aridaman Pandit

Rendered fromRegEnrich.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-07-21
Started: 2020-03-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DeaSet class	DeaSet-class
dimention of `TopNetwork` object	dim,TopNetwork-method
Enrich class	Enrich-class
Inference the name of results of DESeq analysis by a formula (or model matrix) and sample information	getResultsNames
head or tail of Score object	head,Score-method tail,Score-method
Example RNAseq dataset [Human]	Lyme_GSE63085
DeaSet object creator	newDeaSet
TopNetwork object creator	newTopNetwork
Plot results of FET/GSEA enrichment analysis	plot_Enrich plot_Enrich,RegenrichSet-method
Compare the orders of two vectors	plotOrders
Plot regulator and its targets expression	plotRegTarExpr
Plot soft power for WGCNA analysis	plotSoftPower
Print Score object	print.Score
Differential expression analysis step	regenrich_diffExpr regenrich_diffExpr,RegenrichSet-method
Enrichment analysis step	regenrich_enrich regenrich_enrich,RegenrichSet-method
Regulator-target network inference step	regenrich_network regenrich_network,RegenrichSet-method regenrich_network<- regenrich_network<-,RegenrichSet,data.frame-method regenrich_network<-,RegenrichSet,TopNetwork-method
Regulator scoring and ranking	regenrich_rankScore regenrich_rankScore,RegenrichSet-method
RegenrichSet object creator	RegenrichSet
RegenrichSet class	RegenrichSet-class
Result accessor functions	results_DEA results_enrich results_expr results_score results_topNet
Score class	newScore Score-class
methods of generic function "show"	show,DeaSet-method show,Enrich-method show,RegenrichSet-method show,Score-method show,TopNetwork-method
Human gene regulators	TFs
TopNetwork class	TopNetwork-class