WGCNA

WGCNA is an R software package containing a collection of functions for analyzing weighted correlation networks, such as network construction, module detection, gene selection, calculations of topological properties, data simulation, and visualization. See also crosslinkWGCNA

Topic

Gene expression

Detail

  • Operation: Gene expression correlation

  • Software interface: Library

  • Language: R

  • License: GNU General Public License v2 | v3

  • Cost: Free

  • Version name: 1.71

  • Credit: The work was supported in part by grants P50CA092131, 5P30CA016042-28, and NS050151-01.

  • Input: -

  • Output: -

  • Contact: Peter Langfelder Peter.Langfelder@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Strategies for aggregating gene expression data: the collapseRows R function
  • Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR, Horvath S. Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics. 2011 Aug 4;12:322. doi: 10.1186/1471-2105-12-322. PMID: 21816037; PMCID: PMC3166942.
  • https://doi.org/10.1186/1471-2105-12-322
  • PMID: 21816037
  • PMC: PMC3166942
  • WGCNA: an R package for weighted correlation network analysis.
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559. PMID: 19114008; PMCID: PMC2631488.
  • https://doi.org/10.1186/1471-2105-9-559
  • PMID: 19114008
  • PMC: PMC2631488
  • Is my network module preserved and reproducible?
  • Langfelder P, Luo R, Oldham MC, Horvath S. Is my network module preserved and reproducible? PLoS Comput Biol. 2011 Jan 20;7(1):e1001057. doi: 10.1371/journal.pcbi.1001057. PMID: 21283776; PMCID: PMC3024255.
  • https://doi.org/10.1371/journal.pcbi.1001057
  • PMID: 21283776
  • PMC: PMC3024255
  • A general framework for weighted gene co-expression network analysis
  • Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4:Article17. doi: 10.2202/1544-6115.1128. Epub 2005 Aug 12. PMID: 16646834.
  • https://doi.org/10.2202/1544-6115.1128
  • PMID: 16646834
  • PMC: -
  • A direct approach to estimating false discovery rates conditional on covariates
  • Boca SM, Leek JT. A direct approach to estimating false discovery rates conditional on covariates. PeerJ. 2018 Dec 10;6:e6035. doi: 10.7717/peerj.6035. PMID: 30581661; PMCID: PMC6292380.
  • https://doi.org/10.7717/peerj.6035
  • PMID: 30581661
  • PMC: PMC6292380

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