Topological overlap matrix similarity and dissimilarity
Estimate the true trait underlying a list of surrogate markers.
Allow and disable multi-threading for certain WGCNA calculations
Automatic network construction and module detection
Accuracy measures for a 2x2 confusion matrix or for vectors of predicted and observed values.
Check adjacency matrix
Function to plot kME values between two comparable data sets.
Fast colunm- and row-wise quantile of a matrix.
Add vertical ``guide lines'' to a dendrogram plot
Stem Cell-Related Genes with Corresponding Gene Markers
Align expression data with given vector
Deviance- and martingale residuals from a Cox regression model
Prediction of Weighted Mutual Information Adjacency Matrix by Correlation
consensusProjectiveKMeans
Consensus projective K-means (pre-)clustering of expression data
Graphical representation of the Topological Overlap Matrix
Produce a labeled heatmap plot
Add trait information to multi-set module eigengene structure
Calculate consensus kME (eigengene-based connectivities) across multiple data sets.
Projective K-means (pre-)clustering of expression data
Calculate network adjacency based on natural cubic spline regression
Calculation of block-wise topological overlaps
Consensus network (topological overlap).
Qunatification of success of gene screening
Attempt to calculate an appropriate block size to maximize efficiency of block-wise calcualtions.
Filter genes with too many missing entries across multiple sets
Branch split based on dissimilarity.
Calculate module eigengenes.
automaticNetworkScreening
One-step automatic network gene screening
Calculation of biweight midcorrelations and associated p-values
Iterative filtering of samples and genes with too many missing entries across multiple data sets
Adjacency matrix based on polynomial regression
Number of present data entries.
populationMeansInAdmixture
Estimate the population-specific mean values in an admixed population.
Check structure and retrieve sizes of a group of datasets.
Chooses a single hub gene in each module
Weights used in biweight midcovariance
Blue-white-red color sequence
Iterative garbage collection.
Put single-set data into a form useful for multiset calculations.
Get and set column names in a multiData structure.
Inline display of progress
Inline display of progress
Blood Cell Types with Corresponding Gene Markers
Relabel module labels to best match the given reference labels
Put close eigenvectors next to each other
Determine whether the supplied object is a valid multiData structure
Union and intersection of multiple sets
Threshold for module merging
conformityBasedNetworkConcepts
Calculation of conformity-based network concepts.
standardScreeningBinaryTrait
Standard screening for binatry traits
Transform numerical labels into normal order.
Bar plots of data across two splitting parameters
Network gene screening with an external gene significance measure
Fixed-height cut of a dendrogram.
Chooses the top hub gene in each module
Generalized Topological Overlap Measure
Determines significant overlap between modules in two networks based on kME tables.
Preservation of eigengene correlations
Green-black-red color sequence
Export network to Cytoscape
setCorrelationPreservation
Summary correlation preservation measure
Estimate the proportion of pure populations in an admixed population based on marker expression
values.
Select, swap, or reflect branches in a dendrogram.
preservationNetworkConnectivity
Network preservation calculations
Branch dissimilarity based on eigennodes (eigengenes).
Hubgene significance
Red-white-green color sequence
Pathways with Corresponding Gene Markers - Compiled by Mike Palazzolo and Jim Wang from CHDI
Filter genes with too many missing entries
Clustering coefficient calculation
automaticNetworkScreeningGS
One-step automatic network gene screening with external gene significance
Barplot with text or color labels.
Convert a list to a multiData structure and vice-versa.
Constant-height tree cut
Gene Markers for Regions of the Human Brain
Consensus clustering based on topological overlap and hierarchical clustering
Biweight Midcorrelation
Immune Pathways with Corresponding Gene Markers
nearestNeighborConnectivityMS
Connectivity to a constant number of nearest neighbors across multiple data sets
Co-clustering measure of cluster preservation between two clusterings
Calculations of network concepts
Export network data in format readable by VisANT
Branch split.
fundamentalNetworkConcepts
Calculation of fundamental network concepts from an adjacency matrix.
Topological overlap for a subset of the whole set of genes
orderBranchesUsingHubGenes
Optimize dendrogram using branch swaps and reflections.
Analysis of scale free topology for soft-thresholding
Selects one representative row per group based on kME
Add error bars to a barplot.
Labeled heatmap divided into several separate plots.
Hard-thresholding adjacency function
Measure enrichment between inputted and user-defined lists
Put close eigenvectors next to each other in several sets.
Filter samples with too many missing entries
Add grid lines to an existing plot.
coClustering.permutationTest
Permutation test for co-clustering
Conformity and module based decomposition of a network adjacency matrix.
Calculate module eigengenes.
branchSplitFromStabilityLabels
Branch split (dissimilarity) statistic derived from labels determined from a stability study
Create a multiData structure.
Simulate small modules
Identification of genes related to a trait
Red and Green Color Image of Correlation Matrix
Sigmoid-type adacency function.
Reconstruct a symmetric matrix from a distance (lower-triangular) representation
Select one representative row per group
Student asymptotic p-value for correlation
If possible, simplify a multiData structure to a 3-dimensional array.
Topological overlap matrix
Number of sets in a multi-set variable
Turn a matrix into a vector of non-redundant components
Calculation of correlations and associated p-values
Convert numerical labels to colors.
Colors this library uses for labeling modules.
nearestNeighborConnectivity
Connectivity to a constant number of nearest neighbors
Transpose a big matrix or data frame
Break long character strings into multiple lines
Merge close modules in gene expression data
Consensus dissimilarity of module eigengenes.
Calculation of intramodular connectivity
Keep probes that are shared among given data sets
Green-white-red color sequence
Fisher's asymptotic p-value for correlation
Pairwise scatterplots of eigengenes
Get the prefix used to label module eigengenes.
Repeat blockwise consensus module detection from pre-calculated data
Fast calculations of Pearson correlation.
Pad numbers with leading zeros to specified total width
Calculation of fitting statistics for evaluating scale free topology fit.
Simulate eigengene network from a causal model
Annotated clustering dendrogram of microarray samples
Boxplot annotated by a Kruskal-Wallis p-value
Merge modules and reassign genes using kME.
Signed eigengene-based connectivity
Calculation of unsigned adjacency
Label scatterplot points
qvalue convenience wrapper
Simulate multi-set expression data
Red and Green Color Specification
Show colors used to label modules
Standard error of the mean of a given vector.
Apply a function to each set in a multiData structure.
Prepend a comma to a non-empty string
Calculate weighted adjacency matrices based on mutual information
Dendrogram plot with color annotation of objects
Topological overlap for a subset of a whole set of genes
Calculation of module preservation statistics
Simplified simulation of expression data
Simulation of expression data
Repeat blockwise module detection from pre-calculated data
Red and Green Color Image of Data Matrix
Calculate network adjacency
Opens a graphics window with specified dimensions
multiData.eigengeneSignificance
Eigengene significance across multiple sets
Construct a network from a matrix
Color representation for a numeric variable
Space-less paste
removePrincipalComponents
Remove leading principal components from data
Nearest centroid predictor
Plot color rows in a given order, for example under a dendrogram
Estimate the p-value for ranking consistently high (or low) on multiple lists
Barplot of module significance
Parallel quantile, median, mean
Turn a multiData structure into a single matrix or data frame.
Constant height tree cut using color labels
Estimate the q-values for a given set of p-values
Subset rows and columns in a multiData structure
Voting linear predictor
Simulate a gene co-expression module
Filter samples with too many missing entries across multiple data sets
Scatterplot annotated by regression line and p-value
Divide tasks among workers
Calculates connectivity of a weighted network.
Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value
Rand index of two partitions
Analysis of scale free topology for hard-thresholding.
Proportion of variance explained by eigengenes.
Calculation of GO enrichment (experimental)
Eigengene network plot
Visual check of scale-free topology
Network heatmap plot
relativeCorPredictionSuccess
Compare prediction success
Brain-Related Categories with Corresponding Gene Markers
Empirical Bayes-moderated adjustment for unwanted covariates
Return pre-defined gene lists in several biomedical categories.
Weighted Gene Co-Expression Network Analysis
Removes the grey eigengene from a given collection of eigengenes.
standardScreeningNumericTrait
Standard screening for numeric traits
Apply a function to elements of given multiData structures.
Meta-analysis Z statistic
Iterative filtering of samples and genes with too many missing entries
blockwiseConsensusModules
Find consensus modules across several datasets.
standardScreeningCensoredTime
Standard Screening with regard to a Censored Time Variable
Scatterplot with density
Meta-analysis of binary and continuous variables
Set attributes on each component of a multiData structure
Calculate overlap of modules
Shorten given character strings by truncating at a suitable separator.