WGCNA1.73 package

Accuracy measures for a 2x2 confusion matrix or for vectors of predict...

Add error bars to a barplot.

Add grid lines to an existing plot.

Add vertical ``guide lines'' to a dendrogram plot

Add trait information to multi-set module eigengene structure

Adjacency matrix based on polynomial regression

Calculate network adjacency

Calculate network adjacency based on natural cubic spline regression

Prediction of Weighted Mutual Information Adjacency Matrix by Correlat...

Align expression data with given vector

Divide tasks among workers

Allow and disable multi-threading for certain WGCNA calculations

One-step automatic network gene screening

One-step automatic network gene screening with external gene significa...

Various basic operations on BlockwiseData objects.

Biweight Midcorrelation

Calculation of biweight midcorrelations and associated p-values

Weights used in biweight midcovariance

Turn categorical columns into sets of binary indicators

Turn a categorical variable into a set of binary indicators

Attempt to calculate an appropriate block size to maximize efficiency ...

Find consensus modules across several datasets.

Calculation of block-wise topological overlaps

Automatic network construction and module detection

Blue-white-red color sequence

Branch dissimilarity based on eigennodes (eigengenes).

Branch split based on dissimilarity.

Branch split.

Branch split (dissimilarity) statistics derived from labels determined...

Check adjacency matrix

Check structure and retrieve sizes of a group of datasets.

Chooses a single hub gene in each module

Chooses the top hub gene in each module

Clustering coefficient calculation

Permutation test for co-clustering

Co-clustering measure of cluster preservation between two clusterings

Select one representative row per group

Selects one representative row per group based on kME

Iterative garbage collection.

Fast colunm- and row-wise quantile of a matrix.

Calculation of conformity-based network concepts.

Conformity and module based decomposition of a network adjacency matri...

Calculation of a (single) consenus with optional data calibration.

Consensus clustering based on topological overlap and hierarchical clu...

Calculate consensus kME (eigengene-based connectivities) across multip...

Consensus dissimilarity of module eigengenes.

Put close eigenvectors next to each other in several sets.

Consensus projective K-means (pre-)clustering of expression data

Consensus selection of group representatives

Consensus network (topological overlap).

Get all elementary inputs in a consensus tree

Convert character columns that represent numbers to numeric

Fast calculations of Pearson correlation.

Calculation of correlations and associated p-values

Qunatification of success of gene screening

Fisher's asymptotic p-value for correlation

Student asymptotic p-value for correlation

Preservation of eigengene correlations

Deviance- and martingale residuals from a Cox regression model

Constant-height tree cut

Constant height tree cut using color labels

Show colors used to label modules

Threshold for module merging

Empirical Bayes-moderated adjustment for unwanted covariates

Export network to Cytoscape

Export network data in format readable by VisANT

Turn non-numeric columns into factors

Put single-set data into a form useful for multiset calculations.

Break long character strings into multiple lines

Calculation of fundamental network concepts from an adjacency matrix.

Calculation of GO enrichment (experimental)

Filter genes with too many missing entries

Filter genes with too many missing entries across multiple sets

Filter samples with too many missing entries

Iterative filtering of samples and genes with too many missing entries

Iterative filtering of samples and genes with too many missing entries...

Filter samples with too many missing entries across multiple data sets

Green-black-red color sequence

Green-white-red color sequence

Generalized Topological Overlap Measure

Hierarchical consensus calculation

Calculation of measures of fuzzy module membership (KME) in hierarchic...

Hierarchical consensus calculation of module eigengene dissimilarity

Hierarchical consensus network construction and module identification

Calculation of hierarchical consensus topological overlap matrix

Merge close (similar) hierarchical consensus modules

Hubgene significance

Impute missing data separately in each module

Calculate individual correlation network matrices

Inline display of progress

Calculation of intramodular connectivity

Determine whether the supplied object is a valid multiData structure

Keep probes that are shared among given data sets

Function to plot kME values between two comparable data sets.

Barplot with text or color labels.

Labeled heatmap divided into several separate plots.

Produce a labeled heatmap plot

Label scatterplot points

Convert numerical labels to colors.

Convert a list to a multiData structure and vice-versa.

Reconstruct a symmetric matrix from a distance (lower-triangular) repr...

Relabel module labels to best match the given reference labels

Construct a network from a matrix

Merge close modules in gene expression data

Meta-analysis of binary and continuous variables

Meta-analysis Z statistic

Fast joint calculation of row- or column-wise minima and indices of mi...

Modified Bisquare Weights

Get the prefix used to label module eigengenes.

Calculate module eigengenes.

Merge modules and reassign genes using kME.

Fixed-height cut of a dendrogram.

Calculation of module preservation statistics

Apply a function to each set in a multiData structure.

Apply a function to elements of given multiData structures.

Turn a multiData structure into a single matrix or data frame.

Set attributes on each component of a multiData structure

Get and set column names in a multiData structure.

If possible, simplify a multiData structure to a 3-dimensional array.

Subset rows and columns in a multiData structure

Eigengene significance across multiple sets

Create a multiData structure.

Analogs of grep(l) and (g)sub for multiple patterns and relacements

Calculate module eigengenes.

Union and intersection of multiple sets

Calculate weighted adjacency matrices based on mutual information

Nearest centroid predictor

Connectivity to a constant number of nearest neighbors

Connectivity to a constant number of nearest neighbors across multiple...

Calculations of network concepts

Identification of genes related to a trait

Network gene screening with an external gene significance measure

Create a list holding information about dividing data into blocks

Create, merge and expand BlockwiseData objects

Create a list holding consensus calculation options.

Create a new consensus tree

Creates a list of correlation options.

Create a list of network construction arguments (options).

Transform numerical labels into normal order.

Number of present data entries.

Number of sets in a multi-set variable

Color representation for a numeric variable

Optimize dendrogram using branch swaps and reflections.

Put close eigenvectors next to each other

Order module eigengenes by their hierarchical consensus similarity

Calculate overlap of modules

Determines significant overlap between modules in two networks based o...

Analysis of scale free topology for hard-thresholding.

Analysis of scale free topology for soft-thresholding

Annotated clustering dendrogram of microarray samples

Plot color rows in a given order, for example under a dendrogram

Red and Green Color Image of Correlation Matrix

Dendrogram plot with color annotation of objects

Eigengene network plot

Red and Green Color Image of Data Matrix

Pairwise scatterplots of eigengenes

Barplot of module significance

Plot multiple histograms in a single plot

Network heatmap plot

Estimate the population-specific mean values in an admixed population.

Parallel quantile, median, mean

Prepend a comma to a non-empty string

Pad numbers with leading zeros to specified total width

Network preservation calculations

Projective K-means (pre-)clustering of expression data

Estimate the proportion of pure populations in an admixed population b...

Proportion of variance explained by eigengenes.

Iterative pruning and merging of (hierarchical) consensus modules

Prune (hierarchical) consensus modules by removing genes with low eige...

Estimate the q-values for a given set of p-values

qvalue convenience wrapper

Rand index of two partitions

Estimate the p-value for ranking consistently high (or low) on multipl...

Repeat blockwise module detection from pre-calculated data

Repeat blockwise consensus module detection from pre-calculated data

Red-white-green color sequence

Compare prediction success

Removes the grey eigengene from a given collection of eigengenes.

Remove leading principal components from data

Replace missing values with a constant.

Return pre-defined gene lists in several biomedical categories.

Red and Green Color Specification

Blockwise module identification in sampled data

Hierarchical consensus module identification in sampled data

Calculation of fitting statistics for evaluating scale free topology f...

Visual check of scale-free topology

Select columns with the lowest consensus number of missing data

Summary correlation preservation measure

Shorten given character strings by truncating at a suitable separator.

Sigmoid-type adacency function.

Signed eigengene-based connectivity

Round numeric columns to given significant digits.

Hard-thresholding adjacency function

Simple calculation of a single consenus

Simple hierarchical consensus calculation

Simulation of expression data

Simplified simulation of expression data

Simulate eigengene network from a causal model

Simulate a gene co-expression module

Simulate multi-set expression data

Simulate small modules

Opens a graphics window with specified dimensions

Cluter merging with size restrictions

Calculates connectivity of a weighted network.

Space-less paste

Colors this library uses for labeling modules.

Standard screening for binatry traits

Standard Screening with regard to a Censored Time Variable

Standard screening for numeric traits

Standard error of the mean of a given vector.

Bar plots of data across two splitting parameters

Topological overlap for a subset of a whole set of genes

Select, swap, or reflect branches in a dendrogram.

Graphical representation of the Topological Overlap Matrix

Topological overlap matrix similarity and dissimilarity

Topological overlap matrix

Transpose a big matrix or data frame

Estimate the true trait underlying a list of surrogate markers.

Calculation of unsigned adjacency

Measure enrichment between inputted and user-defined lists

Turn a matrix into a vector of non-redundant components

Topological overlap for a subset of the whole set of genes

Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value

Boxplot annotated by a Kruskal-Wallis p-value

Scatterplot with density

Scatterplot annotated by regression line and p-value

Voting linear predictor