Man pages for jonalim/mfBiclust
Pipelines for Bi-Clustering Using Matrix Factorization

addStratAdd a BiclusterStrategy to a BiclusterExperiment
als_nmfAlternating-least-squares non-negative matrix approximation
auto_bcvUse BCV to estimate the optimal k until convergence
bcNamesNames of biclusters in this BiclusterStrategy
bcvCalculate bi-cross-validation
BiclusterExperimentConstruct a container for biclustering runs
BiclusterExperiment-classClass "BiclusterExperiment" for data and biclusters
biclusterGUIExplore a BiclusterExperiment
biclusterMatrix2ListConvert logical matrices to two lists of rows and columns
bicluster-methodsBiclustering algorithms
biclusterNumbers2membershipMatricesConvert row and column numbers to a matrix representation
BiclusterStrategy-classClass "BiclusterStrategy" for biclusters
cancer_benchmarkGene expression datasets for benchmarking classification...
cleanClean a matrix or BiclusterExperiment
clusteredFeaturesBicluster-feature matrix
clusteredSamplesSample-bicluster matrix
factorHeatmapPlot a heatmap showing bicluster membership of samples or...
featureFactorFeature matrix factor
featureThreshFeature thresholds
filter.biclustFilter biclusters by overlap and quantity
genericFactorization-classA pair of matrix factors
genericFit-classA biclustering algorithm result
genSimDataSimulate an omics dataset with biclusters
getStratGet a BiclusterStrategy
matrixHeatmapQuickly preview a matrix as a heatmap
methodThe biclustering algorithm used
mfBiclustMatrix-factorization biclustering toolbox
nameName of a BiclusterStrategy
nclustNumber of biclusters
nipals_pcaPrincipal component dimensionality reduction using NIPALS
otsuHelperCalculate Otsu thresholds on each column of a matrix
overlapCalculate overlaps between every pair of biclusters.
plotExpression plot
plotDistDistance heatmap
plotThresholdThreshold plot
sampleFactorSample matrix factor
sampleThreshSample thresholds
simdataSimulated bicluster datasets
sizesCalculate bicluster sizes
strategiesResults of biclustering runs on a single dataset
svd_pcaPrincipal component dimensionality reduction using SVD
threshAlgoAlgorithm used to calculate a threshold
thresholdApply thresholds to a score or loading matrix
union.biclustCreate a binary matrix describing a union of biclusters
wipeWipe biclustering results
wipeExceptWipe all biclustering results except one
yeast_benchmarkGene expression datasets for benchmarking detection of...
jonalim/mfBiclust documentation built on Jan. 17, 2019, 7:04 a.m.