Package: oppar 1.35.0

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:Chenwei Wang [aut], Alperen Taciroglu [aut], Stefan R Maetschke [aut], Colleen C Nelson [aut], Mark Ragan [aut], Melissa Davis [aut], Soroor Hediyeh zadeh [cre], Momeneh Foroutan [ctr]

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oppar.pdf |oppar.html✨
oppar/json (API)
NEWS

# Install 'oppar' in R:
install.packages('oppar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • bcm - Breast cancer metastases from different anatomical sites
  • eset - Tomlins et al. Prostate Cancer data
  • maupin - Maupin's TGFb data and a TGFb gene signature

On BioConductor:oppar-1.35.0(bioc 3.21)oppar-1.34.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

pathwaysgenesetenrichmentsystemsbiologygeneexpressionsoftware

3.30 score 3 scripts 194 downloads 5 exports 95 dependencies

Last updated 21 days agofrom:f75865223c. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64WARNINGNov 19 2024
R-4.5-linux-x86_64WARNINGNov 19 2024
R-4.4-win-x86_64WARNINGNov 19 2024
R-4.4-mac-x86_64WARNINGNov 19 2024
R-4.4-mac-aarch64WARNINGNov 19 2024
R-4.3-win-x86_64WARNINGNov 19 2024
R-4.3-mac-x86_64WARNINGNov 19 2024
R-4.3-mac-aarch64WARNINGNov 19 2024

Exports:getSampleOutliergetSubtypeProbesgsvaopashow

Dependencies:abindannotateAnnotationDbiaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegraphGSEABaseGSVAHDF5ArrayhttrIRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6Rcpprhdf5rhdf5filtersRhdf5librjsonrlangRSQLitersvdS4ArraysS4VectorsScaledMatrixSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxtableXVectorzlibbioc

OPPAR: Outlier Profile and Pathway Analysis in R

Soroor Hediyehzadeh

Rendered fromoppar.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2018-09-06
Started: 2016-04-06

Readme and manuals

Help Manual

Help pageTopics
Breast cancer metastases from different anatomical sitesbcm
Tomlins et al. Prostate Cancer data (GEO: GSE6099)eset
Retrieving outlier genes in samplesgetSampleOutlier getSampleOutlier,matrix,nuchar-method getSampleOutlier,OPPARList,nuchar-method
Retrieving outlier genes from a group of related samplesgetSubtypeProbes getSubtypeProbes,matrix,nuchar-method getSubtypeProbes,OPPARList,nuchar-method
gsvagsva gsva,ExpressionSet,GeneSetCollection-method gsva,ExpressionSet,list-method gsva,matrix,GeneSetCollection-method gsva,matrix,list-method
Maupin's TGFb data and a TGFb gene signaturemaupin
Outlier profile Analysisopa 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