Package: rqubic 1.53.0
Jitao David Zhang
rqubic: Qualitative biclustering algorithm for expression data analysis in R
This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.
Authors:
rqubic_1.53.0.tar.gz
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rqubic.pdf |rqubic.html✨
rqubic/json (API)
NEWS
| # Install 'rqubic' in R: |
| install.packages('rqubic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:rqubic-1.53.0(bioc 3.21)rqubic-1.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:0a9a982909. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:BCconditionCountBCconditionsBCcountBCfeatureCountBCfeaturescombineBiclustsconditionCountconditionseSetDimNamefcFilterfeatureCountfeatureNamesfeaturesgenerateSeedsinfoNumberxColparameterparseQubicBlocksparseQubicCharsparseQubicRulesquantileDiscretizequBiclusterreadBiclusterResultsRowxNumbersampleNamesSvaluewriteQubicInputFile
Dependencies:additivityTestsbiclustBiobaseBiocGenericsclassclicolorspacecpp11dplyrfansifarverflexclustgenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmodeltoolsmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Qualitative biclustering algorithm for expression data analysis | rqubic-package rqubic |
| Combine two or more Biclust objects into one | combineBiclusts combineBiclusts,Biclust,Biclust-method combineBiclusts,list,missing-method combineBiclusts,QUBICBiclusterSet,QUBICBiclusterSet-method combineBiclusts-methods |
| Get dimname from an eSet object | eSetDimName |
| Feature-Condition Filter | fcFilter fcFilter,Biclust-method |
| Feature-Condition Filter | fcFilter-methods |
| Extract features and conditions | BCconditionCount BCconditionCount,Biclust,ANY-method BCconditionCount,Biclust,missing-method BCconditions BCconditions,Biclust,ANY-method BCconditions,Biclust,missing-method BCfeatureCount BCfeatureCount,Biclust,ANY-method BCfeatureCount,Biclust,missing-method BCfeatures BCfeatures,Biclust,ANY-method BCfeatures,Biclust,missing-method conditionCount conditionCount,Biclust-method conditionCount-methods conditions conditions,Biclust-method conditions-methods featureCount featureCount,Biclust-method featureCount-methods featureNames,Biclust-method features features,Biclust-method features-methods sampleNames,Biclust-method |
| Generate seeds for biclustering | generateSeeds generateSeeds,eSet-method generateSeeds,matrix-method generateSeeds-methods |
| Parse QUBIC Command Line Tool Output Files | parseQubicBlocks parseQubicChars parseQubicRules |
| Discretize expression matrix for qualitative biclustering | quantileDiscretize quantileDiscretize,eSet-method quantileDiscretize,matrix-method quantileDiscretize-methods |
| Class "QUBICBiclusterSet" | BCcount BCcount,Biclust-method info info,Biclust,ANY-method info,Biclust,missing-method NumberxCol NumberxCol,Biclust-method parameter parameter,Biclust,character-method parameter,Biclust,missing-method QUBICBiclusterSet-class RowxNumber RowxNumber,Biclust-method show,QUBICBiclusterSet-method Svalue Svalue,eSet,missing-method Svalue,matrix,missing-method Svalue,QUBICBiclusterSet,ANY-method Svalue,QUBICBiclusterSet,missing-method [,Biclust,ANY,missing,missing-method |
| Qualitative Biclustering | quBicluster |
| Import bicluster results from plain text files | readBiclusterResults |
| Write an ExpressionSet object into the file format required by the QUBIC command line tool | writeQubicInputFile |
