Package: GOstats 2.73.0
Bioconductor Package Maintainer
GOstats: Tools for manipulating GO and microarrays
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
Authors:
GOstats_2.73.0.tar.gz
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GOstats.pdf |GOstats.html✨
GOstats/json (API)
| # Install 'GOstats' in R: |
| install.packages('GOstats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GOstats-2.73.0(bioc 3.21)GOstats-2.72.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork
Last updated 3 months agofrom:a8f7238546. Checks:1 ERROR, 6 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 31 2024 |
| R-4.5-win | WARNING | Dec 31 2024 |
| R-4.5-linux | WARNING | Dec 31 2024 |
| R-4.4-win | WARNING | Dec 31 2024 |
| R-4.4-mac | WARNING | Dec 31 2024 |
| R-4.3-win | WARNING | Dec 31 2024 |
| R-4.3-mac | WARNING | Dec 31 2024 |
Exports:annotationcompCorrGraphcompGdistdescriptionenumPairsexpectedCountsgeneCountsgeneIdsgeneIdUniversegeneMappedCountgoDagGOGraphhtmlReporthyperGTestidx2dimnamesinducedTermGraphisTriadmakeGOGraphnotConnoddsRatiosoneGOGraphplotGOTermGraphprobeSetSummarypvaluesreduce2DegreekshortestPathsimLLsimLPsimUIsummarytermGraphstestNametriadCensusuniverseCountsuniverseMappedCount
Dependencies:annotateAnnotationDbiAnnotationForgeaskpassBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemCategoryclicpp11crayoncurlDBIfastmapgenefiltergenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbgraphGSEABasehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RBGLRCurlRgraphvizrlangRSQLiteS4VectorssurvivalsysUCSC.utilsvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tools for manipulating GO and microarrays. | GOstats-package GOstats |
| A function to compute a correlation based graph from Gene Expression Data | compCorrGraph |
| A function to compute the distance between pairs of nodes in a graph. | compGdist |
| Class "GOHyperGResult" | conditional,GOHyperGResult-method expectedCounts,GOHyperGResult-method geneCounts,GOHyperGResult-method geneIdUniverse,GOHyperGResult-method goDag goDag,GOHyperGResult-method GOHyperGResult-class htmlReport,GOHyperGResult-method oddsRatios,GOHyperGResult-method pvalues,GOHyperGResult-method summary,GOHyperGResult-method |
| Defunct Functions in GOstats Package | combGOGraph getGoGraph GOHyperG GOKEGGHyperG GOLeaves GOstats-defunct hyperG2Affy hyperGtable selectedGenes |
| Hypergeometric Tests for GO term association | hyperGTest hyperGTest,GOHyperGParams-method hyperGTest,OBOHyperGParams-method |
| Index to Dimnames | idx2dimnames |
| Construct a GO Graph | makeGOGraph |
| Distance matrices for the BCR/ABL and NEG subgroups. | Bdists Ndists |
| Find genes that are not connected to the others. | notConn |
| Class "OBOHyperGResult" | conditional,OBOHyperGResult-method expectedCounts,OBOHyperGResult-method geneCounts,OBOHyperGResult-method geneIdUniverse,OBOHyperGResult-method goDag,OBOHyperGResult-method htmlReport,OBOHyperGResult-method OBOHyperGResult-class oddsRatios,OBOHyperGResult-method pvalues,OBOHyperGResult-method summary,OBOHyperGResult-method |
| Construct the GO graph given a set of leaves. | GOGraph oneGOGraph |
| Summarize Probe Sets Associated with a hyperGTest Result | probeSetSummary |
| Shortest Path Analysis | shortestPath |
| Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs. | simLL simLP simUI |
| Extraction and Plotting of GO Terms from a GOHyperGResult Object | inducedTermGraph plotGOTermGraph termGraphs |
| Triad Functions | enumPairs isTriad reduce2Degreek triad triadCensus |
