Package: GOstats 2.79.0
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_2.79.0.tar.gz
GOstats_2.79.0.zip(r-4.7)GOstats_2.79.0.zip(r-4.6)GOstats_2.79.0.zip(r-4.5)
GOstats_2.79.0.tgz(r-4.6-any)GOstats_2.79.0.tgz(r-4.5-any)
GOstats_2.79.0.tar.gz(r-4.7-any)GOstats_2.79.0.tar.gz(r-4.6-any)
GOstats_2.79.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-2.79.0(bioc 3.24)GOstats-2.78.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork
Last updated from:f6bbf18acf. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 198 | ||
| linux-devel-x86_64 | WARNING | 376 | ||
| source / vignettes | ERROR | 622 | ||
| linux-release-x86_64 | WARNING | 394 | ||
| macos-release-arm64 | WARNING | 203 | ||
| macos-oldrel-arm64 | WARNING | 282 | ||
| windows-devel | WARNING | 290 | ||
| windows-release | WARNING | 269 | ||
| windows-oldrel | WARNING | 203 | ||
| wasm-release | OK | 178 |
Exports:annotationcompCorrGraphcompGdistdescriptionenumPairsexpectedCountsgeneCountsgeneIdsgeneIdUniversegeneMappedCountgoDagGOGraphhtmlReporthyperGTestidx2dimnamesinducedTermGraphisTriadmakeGOGraphnotConnoddsRatiosoneGOGraphplotGOTermGraphprobeSetSummarypvaluesreduce2DegreekshortestPathsimLLsimLPsimUIsummarytermGraphstestNametriadCensusuniverseCountsuniverseMappedCount
Dependencies:annotateAnnotationDbiAnnotationForgeaskpassBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemCategoryclicpp11crayoncurlDBIfastmapgenefiltergenericsglueGO.dbgraphGSEABasehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RBGLRCurlRgraphvizrlangRSQLiteS4VectorsSeqinfosurvivalsysvctrsXMLxtableXVector
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 |
