Man pages for jonalim/mfBiclust
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... |
