Analysis of Tomlins et al. prostate cancer dataset | Gene Set Enrichment Analysis
Package: oppar 1.41.0
Soroor Hediyeh zadeh
oppar: Outlier profile and pathway analysis in R
The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.
Authors:
oppar_1.41.0.tar.gz
oppar_1.41.0.zip(r-4.7)oppar_1.41.0.zip(r-4.6)oppar_1.41.0.zip(r-4.5)
oppar_1.41.0.tgz(r-4.6-x86_64)oppar_1.41.0.tgz(r-4.6-arm64)oppar_1.41.0.tgz(r-4.5-x86_64)oppar_1.41.0.tgz(r-4.5-arm64)
oppar_1.41.0.tar.gz(r-4.7-arm64)oppar_1.41.0.tar.gz(r-4.7-x86_64)oppar_1.41.0.tar.gz(r-4.6-arm64)oppar_1.41.0.tar.gz(r-4.6-x86_64)
oppar_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
oppar/json (API)
| # Install 'oppar' in R: |
| install.packages('oppar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:oppar-1.41.0(bioc 3.24)oppar-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
pathwaysgenesetenrichmentsystemsbiologygeneexpressionsoftware
Last updated from:892e38d188. Checks:1 NOTE, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 245 | ||
| linux-devel-arm64 | WARNING | 368 | ||
| linux-devel-x86_64 | WARNING | 449 | ||
| source / vignettes | OK | 346 | ||
| linux-release-arm64 | WARNING | 372 | ||
| linux-release-x86_64 | WARNING | 478 | ||
| macos-release-arm64 | WARNING | 235 | ||
| macos-release-x86_64 | WARNING | 501 | ||
| macos-oldrel-arm64 | WARNING | 204 | ||
| macos-oldrel-x86_64 | WARNING | 449 | ||
| windows-devel | WARNING | 357 | ||
| windows-release | WARNING | 360 | ||
| windows-oldrel | WARNING | 329 | ||
| wasm-release | OK | 223 |
Exports:getSampleOutliergetSubtypeProbesgsvaopashow
Dependencies:abindannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelBiocSingularBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluegraphGSEABaseGSVAh5mreadHDF5Arrayhttrhttr2IRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisememusemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Breast cancer metastases from different anatomical sites | bcm |
| Tomlins et al. Prostate Cancer data (GEO: GSE6099) | eset |
| Retrieving outlier genes in samples | getSampleOutlier getSampleOutlier,matrix,nuchar-method getSampleOutlier,OPPARList,nuchar-method |
| Retrieving outlier genes from a group of related samples | getSubtypeProbes getSubtypeProbes,matrix,nuchar-method getSubtypeProbes,OPPARList,nuchar-method |
| gsva | gsva gsva,ExpressionSet,GeneSetCollection-method gsva,ExpressionSet,list-method gsva,matrix,GeneSetCollection-method gsva,matrix,list-method |
| Maupin's TGFb data and a TGFb gene signature | maupin |
| Outlier profile Analysis | opa opa,ExpressionSet-method opa,matrix-method |
| oppar: A package for outlier profile and pathway analysis. | oppar-package oppar |
| A S4 class for the output of OPPAR main function, opa. | $,OPPARList-method OPPARList-class show,OPPARList-method |
