/usr/lib/R/site-library/NMF/INDEX is in r-cran-nmf 0.20.6-1.
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Nonnegative Least-Squares
NMF-class Generic Interface for Nonnegative Matrix
Factorisation Models
NMF-defunct Defunct Functions and Classes in the NMF
Package
NMF-deprecated Deprecated Functions in the Package NMF
NMF-package Algorithms and framework for Nonnegative Matrix
Factorization (NMF).
NMFList-class Class for Storing Heterogeneous NMF fits
NMFOffset-class NMF Model - Nonnegative Matrix Factorization
with Offset
NMFSeed 'NMFSeed' is a constructor method that
instantiate 'NMFSeed' objects.
NMFSeed-class Base class that defines the interface for NMF
seeding methods.
NMFStop Stopping Criteria for NMF Iterative Strategies
NMFStrategy Factory Method for NMFStrategy Objects
NMFStrategyFunction-class
Interface for Single Function NMF Strategies
NMFStrategyIterative-class
Interface for Algorithms: Implementation for
Iterative NMF Algorithms
NMFStrategyOctave-class
S4 Interface for Octave-Matlab NMF Algorithms
NMFfit-class Base Class for to store Nonnegative Matrix
Factorisation results
NMFfitX-class Virtual Class to Handle Results from Multiple
Runs of NMF Algorithms
NMFfitX1-class Structure for Storing the Best Fit Amongst
Multiple NMF Runs
NMFfitXn-class Structure for Storing All Fits from Multiple
NMF Runs
NMFns-class NMF Model - Nonsmooth Nonnegative Matrix
Factorization
NMFstd-class NMF Model - Standard model
[,NMF-method Sub-setting NMF Objects
advanced-NMF Advanced Usage of the Package NMF
aheatmap Annotated Heatmaps
algorithm,NMFList-method
Returns the method names used to compute the
NMF fits in the list. It returns 'NULL' if the
list is empty.
algorithm,NMFStrategyOctave-method
Returns the name of the Octave/Matlab function
that implements the NMF algorithm - as stored
in slot 'algorithm'.
algorithmic-NMF Generic Interface for Algorithms
basis Accessing NMF Factors
basiscor Correlations in NMF Models
basisnames Dimension names for NMF objects
bioc-NMF Specific NMF Layer for Bioconductor
canFit Testing Compatibility of Algorithm and Models
compare-NMF Comparing Results from Different NMF Runs
connectivity Clustering Connectivity and Consensus Matrices
consensus,NMFfitX1-method
Returns the consensus matrix computed while
performing all NMF runs, amongst which 'object'
was selected as the best fit.
consensus,NMFfitXn-method
Computes the consensus matrix of the set of
fits stored in 'object', as the mean
connectivity matrix across runs.
consensushc Hierarchical Clustering of a Consensus Matrix
cophcor Cophenetic Correlation Coefficient
deviance Distances and Objective Functions
dispersion Dispersion of a Matrix
esGolub Golub ExpressionSet
fcnnls Fast Combinatorial Nonnegative Least-Square
featureScore Feature Selection in NMF Models
fit Extracting Fitted Models
fitted Fitted Matrix in NMF Models
getRNG1 Extracting RNG Data from NMF Objects
heatmap-NMF Heatmaps of NMF Factors
ibterms Fixed Terms in NMF Models
is.nmf Testing NMF Objects
match_atrack Extending Annotation Vectors
methods-NMF Registry for NMF Algorithms
nbasis Dimension of NMF Objects
nmf Running NMF algorithms
nmf.equal Testing Equality of NMF Models
nmfAlgorithm Listing and Retrieving NMF Algorithms
nmfAlgorithm.SNMF_R NMF Algorithm - Sparse NMF via Alternating NNLS
nmfApply Apply Function for NMF Objects
nmfCheck Checking NMF Algorithm
nmfEstimateRank Estimate Rank for NMF Models
nmfFormals Showing Arguments of NMF Algorithms
nmfModel Factory Methods NMF Models
nmfObject Updating NMF Objects
nmfReport Run NMF Methods and Generate a Report
nmfSeed Seeding Strategies for NMF Algorithms
nmf_update.KL.h NMF Multiplicative Updates for Kullback-Leibler
Divergence
nmf_update.brunet_R NMF Algorithm/Updates for Kullback-Leibler
Divergence
nmf_update.euclidean.h
NMF Multiplicative Updates for Euclidean
Distance
nmf_update.euclidean_offset.h
NMF Multiplicative Update for NMF with Offset
Models
nmf_update.lee_R NMF Algorithm/Updates for Frobenius Norm
nmf_update.lsnmf Multiplicative Updates for LS-NMF
nmf_update.ns NMF Multiplicative Update for Nonsmooth
Nonnegative Matrix Factorization (nsNMF).
nneg Transforming from Mixed-sign to Nonnegative
Data
objective,NMFfit-method
Returns the objective function associated with
the algorithm that computed the fitted NMF
model 'object', or the objective value with
respect to a given target matrix 'y' if it is
supplied.
offset,NMFOffset-method
Offsets in NMF Models with Offset
offset,NMFfit-method Returns the offset from the fitted model.
options-NMF NMF Package Specific Options
parallel-NMF Utilities for Parallel Computations
plot,NMFfit,missing-method
Plots the residual track computed at regular
interval during the fit of the NMF model 'x'.
predict Clustering and Prediction
profplot Plotting Expression Profiles
purity Purity and Entropy of a Clustering
randomize Randomizing Data
residuals Residuals in NMF Models
rmatrix Generating Random Matrices
rnmf Generating Random NMF Models
rss Residual Sum of Squares and Explained Variance
runtime,NMFList-method
Returns the CPU time required to compute all
NMF fits in the list. It returns 'NULL' if the
list is empty. If no timing data are available,
the sequential time is returned.
runtime.all,NMFfitXn-method
Returns the CPU time used to perform all the
NMF fits stored in 'object'.
scale.NMF Rescaling NMF Models
seed Interface for NMF Seeding Methods
setNMFMethod Registering NMF Algorithms
setupBackend Computational Setup Functions
show,NMF-method Show method for objects of class 'NMF'
show,NMFList-method Show method for objects of class 'NMFList'
show,NMFOffset-method Show method for objects of class 'NMFOffset'
show,NMFSeed-method Show method for objects of class 'NMFSeed'
show,NMFStrategyIterative-method
Show method for objects of class
'NMFStrategyIterative'
show,NMFfit-method Show method for objects of class 'NMFfit'
show,NMFfitX-method Show method for objects of class 'NMFfitX'
show,NMFfitX1-method Show method for objects of class 'NMFfitX1'
show,NMFfitXn-method Show method for objects of class 'NMFfitXn'
show,NMFns-method Show method for objects of class 'NMFns'
silhouette.NMF Silhouette of NMF Clustering
smoothing Smoothing Matrix in Nonsmooth NMF Models
sparseness Sparseness
staticVar Get/Set a Static Variable in NMF Algorithms
summary Assessing and Comparing NMF Models
syntheticNMF Simulating Datasets
t.NMF Transformation NMF Model Objects
utils-NMF Utility Function in the NMF Package
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