Package: consensusOV 1.29.0
Benjamin Haibe-Kains
consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer
This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
Authors:
consensusOV_1.29.0.tar.gz
consensusOV_1.29.0.zip(r-4.5)consensusOV_1.29.0.zip(r-4.4)consensusOV_1.29.0.zip(r-4.3)
consensusOV_1.29.0.tgz(r-4.4-any)consensusOV_1.29.0.tgz(r-4.3-any)
consensusOV_1.29.0.tar.gz(r-4.5-noble)consensusOV_1.29.0.tar.gz(r-4.4-noble)
consensusOV_1.29.0.tgz(r-4.4-emscripten)consensusOV_1.29.0.tgz(r-4.3-emscripten)
consensusOV.pdf |consensusOV.html✨
consensusOV/json (API)
NEWS
| # Install 'consensusOV' in R: |
| install.packages('consensusOV', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bhklab/consensusov/issues
- GSE14764.eset - Sample ExpressionSet from MetaGxOvarian
On BioConductor:consensusOV-1.29.0(bioc 3.21)consensusOV-1.27.0(bioc 3.20)
classificationclusteringdifferentialexpressiongeneexpressionmicroarraytranscriptomicscancer-datacancer-genomicscancer-researchexpression-databaseovarian-cancer
Last updated 23 days agofrom:fcae035631. Checks:OK: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | WARNING | Nov 08 2024 |
| R-4.5-linux | WARNING | Nov 08 2024 |
| R-4.4-win | WARNING | Nov 08 2024 |
| R-4.4-mac | OK | Nov 08 2024 |
| R-4.3-win | WARNING | Nov 08 2024 |
| R-4.3-mac | OK | Nov 08 2024 |
Exports:get.bentink.subtypesget.consensus.subtypesget.hao.subtypesget.helland.subtypesget.konecny.subtypesget.subtypesget.verhaak.subtypesmargin
Dependencies:abindAIMSamapannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularbiomaRtBiostringsbitbit64blobbootstrapcachemclasscliclustercodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdiagramdigestdplyre1071fansifastmapfilelockformatRfutile.loggerfutile.optionsfuturefuture.applygdatagenefugenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglobalsgluegraphGSEABaseGSVAgtoolsHDF5Arrayhmshttrhttr2iC10iC10TrainingDataimputeipredIRangesirlbajsonliteKEGGRESTKernSmoothlambda.rlatticelavalifecyclelimmalistenvmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimennetnumDerivopensslpamrparallellypillarpkgconfigplogrpngprettyunitsprodlimprogressprogressrproxypurrrR6randomForestrappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangrmetarpartRSQLitersvdS4ArraysS4VectorsScaledMatrixshapeSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentSQUAREMstatmodstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2xtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Merging all individual esets and merging them into a big eset | dataset.merging |
| Get ovarian cancer subtypes as defined by Bentink et al., 2012 | get.bentink.subtypes |
| Get consensusOV ovarian cancer subtypes | get.consensus.subtypes margin |
| Get ovarian cancer subtypes as defined by Hao et al., 2017 | get.hao.subtypes |
| Get ovarian cancer subtypes as defined by Helland et al., 2011 | get.helland.subtypes |
| Get ovarian cancer subtypes as defined by Konecny et al., 2014 | get.konecny.subtypes |
| Get ovarian cancer subtypes | get.subtypes |
| Get ovarian cancer subtypes as defined by Verhaak et al., 2013 | get.verhaak.subtypes |
| Sample ExpressionSet from MetaGxOvarian | GSE14764.eset |
