Package: GeneNetworkBuilder 1.47.0

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_1.47.0.tar.gz
GeneNetworkBuilder_1.47.0.zip(r-4.5)GeneNetworkBuilder_1.47.0.zip(r-4.4)GeneNetworkBuilder_1.47.0.zip(r-4.3)
GeneNetworkBuilder_1.47.0.tgz(r-4.4-arm64)GeneNetworkBuilder_1.47.0.tgz(r-4.4-x86_64)GeneNetworkBuilder_1.47.0.tgz(r-4.3-arm64)GeneNetworkBuilder_1.47.0.tgz(r-4.3-x86_64)
GeneNetworkBuilder_1.47.0.tar.gz(r-4.5-noble)GeneNetworkBuilder_1.47.0.tar.gz(r-4.4-noble)
GeneNetworkBuilder_1.47.0.tgz(r-4.4-emscripten)GeneNetworkBuilder_1.47.0.tgz(r-4.3-emscripten)
GeneNetworkBuilder.pdf |GeneNetworkBuilder.html✨
GeneNetworkBuilder/json (API)
NEWS

# Install 'GeneNetworkBuilder' in R:
install.packages('GeneNetworkBuilder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.47.0(bioc 3.20)GeneNetworkBuilder-1.46.0(bioc 3.19)

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

bioconductor-package

11 exports 1.00 score 34 dependencies

Last updated 2 months agofrom:d35be9c3cb

Exports:browseNetworkbrowseNetworkOutputbuildNetworkconvertIDexportNetworkfilterNetworknetworkFromGenespolishNetworkrenderBrowseNetworksubsetNetworkuniqueExprsData

Dependencies:base64encBiocGenericsbslibcachemclidigestevaluatefastmapfontawesomefsgluegraphhighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclememoisemimeplyrR6rappdirsRcppRgraphvizrjsonrlangrmarkdownsasstinytexxfunXMLyaml

GeneNetworkBuilder Guide

Jianhong Ou, Lihua Julie Zhu

Rendered fromGeneNetworkBuilder_vignettes.Rmdusingknitr::rmarkdownon Jul 09 2024.

Last update: 2020-01-18
Started: 2016-12-17

Generate Network from a list of gene

Rendered fromGeneNetworkFromGenes.Rmdusingknitr::rmarkdownon Jul 09 2024.

Last update: 2022-10-25
Started: 2018-09-25

Working with BioGRID, STRING

Rendered fromwith.BioGRID.STRING.Rmdusingknitr::rmarkdownon Jul 09 2024.

Last update: 2021-12-02
Started: 2016-12-17