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GoMiner.Rmdusingknitr::rmarkdownPackage: GoMiner 1.3
GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories
In gene-expression microarray studies, for example, one generally obtains a list of dozens or hundreds of genes that differ in expression between samples and then asks 'What does all of this mean biologically?' Alternatively, gene lists can be derived conceptually in addition to experimentally. For instance, one might want to analyze a group of genes known as housekeeping genes. The work of the Gene Ontology (GO) Consortium <geneontology.org> provides a way to address that question. GO organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. The role of 'GoMiner' is to automate the mapping between a list of genes and GO, and to provide a statistical summary of the results as well as a visualization.
Authors:
GoMiner_1.3.tar.gz
GoMiner_1.3.zip(r-4.7)GoMiner_1.3.zip(r-4.6)GoMiner_1.3.zip(r-4.5)
GoMiner_1.3.tgz(r-4.6-any)GoMiner_1.3.tgz(r-4.5-any)
GoMiner_1.3.tar.gz(r-4.7-any)GoMiner_1.3.tar.gz(r-4.6-any)
GoMiner_1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GoMiner/json (API)
| # Install 'GoMiner' in R: |
| install.packages('GoMiner', repos = c('https://barryzee.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cluster52 - GoMiner data set
- GOGOA3small - GoMiner data set
- HCCS66 - GoMiner data set
- Housekeeping_Genes - GoMiner data set
- x_fdr - GoMiner data set
- x_hyper1 - GoMiner data set
- x_m - GoMiner data set
- x_sampleList1 - GoMiner data set
- x_tablePop3 - GoMiner data set
- x_tablePop31 - GoMiner data set
- x_tableSample3 - GoMiner data set
- x_thresh - GoMiner data set
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:0a6433fd9c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 138 | ||
| source / vignettes | OK | 184 | ||
| linux-release-x86_64 | OK | 139 | ||
| macos-release-arm64 | OK | 134 | ||
| macos-oldrel-arm64 | OK | 93 | ||
| windows-devel | OK | 96 | ||
| windows-release | OK | 110 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 114 |
Exports:checkGeneListVsDBFDRGOenrich3GOheatmapGOhypergeometric3GoMinerGOtable3GOthreshhitterBeforeAfterDriverhitters2humanpreprocessDBrandSubsetGeneListRCPDrunGoMinerExamplestrimGOGOA3validHGNCSymbols
Dependencies:bitopscaToolsdata.tablegplotsgtoolsHGNChelperKernSmoothminimalistGODBrandomGODBsplitstackshapevprint
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| checkGeneListVsDB | checkGeneListVsDB |
| GoMiner data set | cluster52 |
| FDR | FDR |
| GOenrich3 | GOenrich3 |
| GoMiner data set | GOGOA3small |
| GOheatmap | GOheatmap |
| GOhypergeometric | GOhypergeometric3 |
| GoMiner | GoMiner |
| GOtable3 | GOtable3 |
| GOthresh | GOthresh |
| GoMiner data set | HCCS66 |
| hitterBeforeAfterDriver | hitterBeforeAfterDriver |
| hitters2 | hitters2 |
| GoMiner data set | Housekeeping_Genes |
| human | human |
| preprocessDB | preprocessDB |
| randSubsetGeneList | randSubsetGeneList |
| RCPD | RCPD |
| runGoMinerExamples | runGoMinerExamples |
| trimGOGOA3 | trimGOGOA3 |
| validHGNCSymbols | validHGNCSymbols |
| GoMiner data set | x_fdr |
| GoMiner data set | x_hyper1 |
| GoMiner data set | x_m |
| GoMiner data set | x_sampleList1 |
| GoMiner data set | x_tablePop3 |
| GoMiner data set | x_tablePop31 |
| GoMiner data set | x_tableSample3 |
| GoMiner data set | x_thresh |
