Pipelines for Bi-Clustering Using Matrix Factorization

addStrat | Add a BiclusterStrategy to a BiclusterExperiment |

als_nmf | Alternating-least-squares non-negative matrix approximation |

auto_bcv | Use BCV to estimate the optimal k until convergence |

bcNames | Names of biclusters in this BiclusterStrategy |

bcv | Calculate bi-cross-validation |

BiclusterExperiment | Construct a container for biclustering runs |

BiclusterExperiment-class | Class "BiclusterExperiment" for data and biclusters |

biclusterGUI | Explore a BiclusterExperiment |

biclusterMatrix2List | Convert logical matrices to two lists of rows and columns |

bicluster-methods | Biclustering algorithms |

biclusterNumbers2membershipMatrices | Convert row and column numbers to a matrix representation |

BiclusterStrategy-class | Class "BiclusterStrategy" for biclusters |

cancer_benchmark | Gene expression datasets for benchmarking classification... |

clean | Clean a matrix or BiclusterExperiment |

clusteredFeatures | Bicluster-feature matrix |

clusteredSamples | Sample-bicluster matrix |

factorHeatmap | Plot a heatmap showing bicluster membership of samples or... |

featureFactor | Feature matrix factor |

featureThresh | Feature thresholds |

filter.biclust | Filter biclusters by overlap and quantity |

genericFactorization-class | A pair of matrix factors |

genericFit-class | A biclustering algorithm result |

genSimData | Simulate an omics dataset with biclusters |

getStrat | Get a BiclusterStrategy |

matrixHeatmap | Quickly preview a matrix as a heatmap |

method | The biclustering algorithm used |

mfBiclust | Matrix-factorization biclustering toolbox |

name | Name of a BiclusterStrategy |

nclust | Number of biclusters |

nipals_pca | Principal component dimensionality reduction using NIPALS |

otsuHelper | Calculate Otsu thresholds on each column of a matrix |

overlap | Calculate overlaps between every pair of biclusters. |

plot | Expression plot |

plotDist | Distance heatmap |

plotThreshold | Threshold plot |

sampleFactor | Sample matrix factor |

sampleThresh | Sample thresholds |

simdata | Simulated bicluster datasets |

sizes | Calculate bicluster sizes |

strategies | Results of biclustering runs on a single dataset |

svd_pca | Principal component dimensionality reduction using SVD |

threshAlgo | Algorithm used to calculate a threshold |

threshold | Apply thresholds to a score or loading matrix |

union.biclust | Create a binary matrix describing a union of biclusters |

wipe | Wipe biclustering results |

wipeExcept | Wipe all biclustering results except one |

yeast_benchmark | Gene expression datasets for benchmarking detection of... |

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