Package: GeneNetworkBuilder 1.55.0

Jianhong Ou

GeneNetworkBuilder: GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

Authors:Jianhong Ou, Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu

GeneNetworkBuilder_1.55.0.tar.gz
GeneNetworkBuilder_1.55.0.zip(r-4.7)GeneNetworkBuilder_1.55.0.zip(r-4.6)GeneNetworkBuilder_1.55.0.zip(r-4.5)
GeneNetworkBuilder_1.55.0.tgz(r-4.6-x86_64)GeneNetworkBuilder_1.55.0.tgz(r-4.6-arm64)GeneNetworkBuilder_1.55.0.tgz(r-4.5-x86_64)GeneNetworkBuilder_1.55.0.tgz(r-4.5-arm64)
GeneNetworkBuilder_1.55.0.tar.gz(r-4.7-arm64)GeneNetworkBuilder_1.55.0.tar.gz(r-4.7-x86_64)GeneNetworkBuilder_1.55.0.tar.gz(r-4.6-arm64)GeneNetworkBuilder_1.55.0.tar.gz(r-4.6-x86_64)
GeneNetworkBuilder_1.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GeneNetworkBuilder/json (API)
NEWS

# Install 'GeneNetworkBuilder' in R:
install.packages('GeneNetworkBuilder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ce.IDsMap - C.elegns gene name to wormbase identifier map
  • ce.interactionmap - Transcript regulatory map of _Caenorhabditis elegans_
  • ce.mapIDs - Map file for converting from wormbase identifier to _Caenorhabditis elegans_ gene name
  • ce.miRNA.map - Micro RNA of _Caenorhabditis elegans_
  • example.data - Example datasets for documentation
  • hs.IDsMap - Map file for converting gene name or sequence name of _Homo sapiens_ to Entrez identifier
  • hs.interactionmap - Transcript regulation map of _Homo sapiens_
  • hs.mapIDs - Map file for converting from Entrez identifier to _Homo sapiens_ gene name
  • hs.miRNA.map - Micro RNA of _Homo sapiens_

On BioConductor:GeneNetworkBuilder-1.55.0(bioc 3.24)GeneNetworkBuilder-1.54.0(bioc 3.23)

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

sequencingmicroarraygraphandnetworkcpp

4.68 score 24 scripts 500 downloads 12 exports 61 dependencies

Last updated from:421346296d. Checks:1 WARNING, 13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING193
linux-devel-arm64OK214
linux-devel-x86_64OK247
source / vignettesOK602
linux-release-arm64OK203
linux-release-x86_64OK266
macos-release-arm64OK151
macos-release-x86_64OK287
macos-oldrel-arm64OK156
macos-oldrel-x86_64OK460
windows-develOK342
windows-releaseOK378
windows-oldrelOK348
wasm-releaseOK183

Exports:browseNetworkbrowseNetworkOutputbuildNetworkconvertIDcy3NetworkexportNetworkfilterNetworknetworkFromGenespolishNetworkrenderBrowseNetworksubsetNetworkuniqueExprsData

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopsbslibcachemcaToolsclicrayoncurldigestevaluatefastmapfontawesomefsgenericsgluegplotsgraphgtoolshighrhtmltoolshtmlwidgetshttrIRdisplayIRkerneljquerylibjsonliteKernSmoothknitrlifecyclememoisemimeopensslpbdZMQpillarplyrR6rappdirsRColorBrewerRcppRCurlRCy3reprRgraphvizrjsonRJSONIOrlangrmarkdownsassstringisystinytexutf8uuidvctrsxfunXMLyaml

GeneNetworkBuilder Guide

Jianhong Ou, Lihua Julie Zhu

Rendered fromGeneNetworkBuilder_vignettes.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-09-12
Started: 2016-12-17

Generate Network from a list of gene

Rendered fromGeneNetworkFromGenes.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-09-12
Started: 2018-09-25