Introduction | Examples of using GeneNetworkBuilder | Quick start | Example using gene expression profile | Example using both gene and miRNA expression profile | Session Info | References
Package: GeneNetworkBuilder 1.54.0
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:
GeneNetworkBuilder_1.54.0.tar.gz
GeneNetworkBuilder_1.54.0.zip(r-4.7)GeneNetworkBuilder_1.54.0.zip(r-4.6)GeneNetworkBuilder_1.54.0.zip(r-4.5)
GeneNetworkBuilder_1.54.0.tgz(r-4.6-x86_64)GeneNetworkBuilder_1.54.0.tgz(r-4.6-arm64)GeneNetworkBuilder_1.54.0.tgz(r-4.5-x86_64)GeneNetworkBuilder_1.54.0.tgz(r-4.5-arm64)
GeneNetworkBuilder_1.54.0.tar.gz(r-4.7-arm64)GeneNetworkBuilder_1.54.0.tar.gz(r-4.7-x86_64)GeneNetworkBuilder_1.54.0.tar.gz(r-4.6-arm64)GeneNetworkBuilder_1.54.0.tar.gz(r-4.6-x86_64)
GeneNetworkBuilder_1.54.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeneNetworkBuilder/json (API)
| # Install 'GeneNetworkBuilder' in R: |
| install.packages('GeneNetworkBuilder', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
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
Last updated from:4be7f397b5 (on RELEASE_3_23). Checks:1 WARNING, 13 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 222 | ||
| linux-devel-arm64 | OK | 266 | ||
| linux-devel-x86_64 | OK | 295 | ||
| source / vignettes | OK | 503 | ||
| linux-release-arm64 | OK | 217 | ||
| linux-release-x86_64 | OK | 258 | ||
| macos-release-arm64 | OK | 187 | ||
| macos-release-x86_64 | OK | 259 | ||
| macos-oldrel-arm64 | OK | 129 | ||
| macos-oldrel-x86_64 | OK | 286 | ||
| windows-devel | OK | 353 | ||
| windows-release | OK | 331 | ||
| windows-oldrel | OK | 345 | ||
| wasm-release | OK | 186 |
Exports:browseNetworkbrowseNetworkOutputbuildNetworkconvertIDcy3NetworkexportNetworkfilterNetworknetworkFromGenespolishNetworkrenderBrowseNetworksubsetNetworkuniqueExprsData
Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopsbslibcachemcaToolsclicrayoncurldigestevaluatefastmapfontawesomefsgenericsgluegplotsgraphgtoolshighrhtmltoolshtmlwidgetshttrIRdisplayIRkerneljquerylibjsonliteKernSmoothknitrlifecyclememoisemimeopensslpbdZMQpillarplyrR6rappdirsRColorBrewerRcppRCurlRCy3reprRgraphvizrjsonRJSONIOrlangrmarkdownsassstringisystinytexutf8uuidvctrsxfunXMLyaml
GeneNetworkBuilder Guide
Last update: 2024-09-12
Started: 2016-12-17
Generate Network from a list of gene
Using data from STRING | Subset the network by gene list | Communicate with cytoscape
Last update: 2024-09-12
Started: 2018-09-25
