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WGCNA: an R package for weighted correlation network analysis
BackgroundCorrelation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing theExpand
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Is My Network Module Preserved and Reproducible?
In many applications, one is interested in determining which of the properties of a network module change across conditions. For example, to validate the existence of a module, it is desirable toExpand
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Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
SUMMARY Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses aExpand
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Functional organization of the transcriptome in human brain
The enormous complexity of the human brain ultimately derives from a finite set of molecular instructions encoded in the human genome. These instructions can be directly studied by exploring theExpand
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Eigengene networks for studying the relationships between co-expression modules
BackgroundThere is evidence that genes and their protein products are organized into functional modules according to cellular processes and pathways. Gene co-expression networks have been used toExpand
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Fast R Functions for Robust Correlations and Hierarchical Clustering.
Many high-throughput biological data analyses require the calculation of large correlation matrices and/or clustering of a large number of objects. The standard R function for calculating PearsonExpand
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A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program
The regenerative capacity of the injured CNS in adult mammals is severely limited, yet axons in the peripheral nervous system (PNS) regrow, albeit to a limited extent, after injury. We reasoned thatExpand
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Integrated genomics and proteomics to define huntingtin CAG length-dependent networks in HD Mice
To gain insight into how mutant huntingtin (mHtt) CAG repeat length modifies Huntington's disease (HD) pathogenesis, we profiled mRNA in over 600 brain and peripheral tissue samples from HD knock-inExpand
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Aging effects on DNA methylation modules in human brain and blood tissue
BackgroundSeveral recent studies reported aging effects on DNA methylation levels of individual CpG dinucleotides. But it is not yet known whether aging-related consensus modules, in the form ofExpand
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Weighted Gene Coexpression Network Analysis: State of the Art
Weighted gene coexpression network analysis (WGCNA) has been applied to many important studies since its introduction in 2005. WGCNA can be used as a data exploratory tool or as a gene screeningExpand
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