Package: biclust 2.0.3.1
Sebastian Kaiser
biclust: BiCluster Algorithms
The main function biclust() provides several algorithms to find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0), spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.
Authors:
biclust_2.0.3.1.tar.gz
biclust_2.0.3.1.tar.gz(r-4.5-noble)biclust_2.0.3.1.tar.gz(r-4.4-noble)
biclust_2.0.3.1.tgz(r-4.4-emscripten)biclust_2.0.3.1.tgz(r-4.3-emscripten)
biclust.pdf |biclust.html✨
biclust/json (API)
NEWS
| # Install 'biclust' in R: |
| install.packages('biclust', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- BicatYeast - BicAT Yeast
- EisenYeast - Eisen Yeast
- SyntrenEcoli - SynTReN E. coli
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:b0162716e1. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 27 2024 |
Exports:additiveVarianceBCBimaxBCCCBCPlaidBCQuestBCQuestmetBCQuestordBCrepBimaxBCSpectralBCXmotifsbiclustbiclustbarchartbiclusterbiclusternumberbiclustmemberBiclustResultbicorderbimax.gridbinarizebinarizeByPercentagebubbleplotChiaKaruturiclustmembercomputeObservedFstatconstantVariancedensityOnesdiagnoseColRowdiagnosticPlotdiagnosticPlot2diagnosticTestdiscretizedrawHeatmapdrawHeatmap2ensembleheatmapBCisoverlappjaccard2jaccardindmultiplicativeVarianceparallelCoordinatesplaid.gridplotclustpredictBimaxshowsignVariancespectralsummarywriteBiclusterResultswriteclust
Dependencies:additivityTestsclassclicolorspacecpp11dplyrfansifarverflexclustgenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmodeltoolsmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The Bimax Bicluster algorithm | BCBimax BCBimax-class BCrepBimax BCrepBimax-class biclust,matrix,BCBimax-method biclust,matrix,BCrepBimax-method Bimax repBimax |
| The CC Bicluster algorithm | BCCC BCCC-class biclust,matrix,BCCC-method CC |
| The Plaid Model Bicluster algorithm | BCPlaid BCPlaid-class biclust,matrix,BCPlaid-method plaid plaid model turner biclustering |
| The Questmotif Bicluster algorithm | BCQuest BCQuest-class BCQuestmet BCQuestmet-class BCQuestord BCQuestord-class biclust,matrix,BCQuest-method biclust,matrix,BCQuestmet-method biclust,matrix,BCQuestord-method Quest |
| The Spectral Bicluster algorithm | BCSpectral BCSpectral-class biclust,matrix,BCSpectral-method Kluger biclustering spectral spectral biclustering |
| The Xmotifs Bicluster algorithm | BCXmotifs BCXmotifs-class biclust,matrix,BCXmotifs-method Xmotif |
| BicAT Yeast | BicatYeast Saccharomices Cerevisiae reduced data matrix yeast microarray reduced data matrix |
| The biclust Method | biclust biclust,matrix,BiclustMethod-method biclust,matrix,character-method biclust,matrix,function-method biclust-method |
| The Biclust Class | Biclust Biclust-class BiclustResult show,Biclust-method summary,Biclust-method |
| Bicluster Barchart | biclustbarchart |
| Extract Bilcuster | bicluster biclusternumber |
| Bicluster Membership Graph | biclustmember bicorder clustmember |
| The BiclustMethod Virtual Class | BiclustMethod BiclustMethod-class |
| Parameter Grid for BCBimax Biclustering | bimax.grid |
| Binarize | binarize binarizeByPercentage densityOnes |
| Bubbleplot | bubble plot bubbleplot star graph |
| Chia and Karuturi Function | ChiaKaruturi |
| Coherence measures | additiveVariance coherence constantVariance multiplicativeVariance signVariance |
| Diagnostic F Statistic Calculation | computeObservedFstat |
| Bootstrap Procedure for Bicluster Diagnostics | diagnoseColRow |
| Diagnostic F Statistics Visualization | diagnosticPlot |
| Diagnostics F Statistiics Visualization | diagnosticPlot2 |
| Testing Procedure for Bicluster Diagnostics | diagnosticTest |
| Create a discret matrix | discretize |
| Draw Heatmap | drawHeatmap drawHeatmap2 heatmap |
| Eisen Yeast | EisenYeast Saccharomices Cerevisiae data matrix yeast microarray data matrix |
| Ensemble Methods for Bicluster Algorithms | ensemble |
| Overlapping Heatmap | heatmapBC |
| Is Bicresult overlapping? | isoverlapp |
| Jaccardind | jaccard2 jaccardind |
| Parallel Coordinates | parallel coordinates parallelCoordinates |
| Parameter Grid for BCPlaid Biclustering | plaid.grid |
| Barplot of Bicluster | plotclust |
| Predict from a BCrepBimax Result | predictBimax |
| SynTReN E. coli | E. coli microarray synthetic data matrix Escherichia Coly data matrix generated by SynTReN SyntrenEcoli |
| writeBiclusterResults | writeBiclusterResults writeBiclusters |
| Write a Bicluster as a Cluster Result | writeclust |