CCLasso

CCLasso is a software tool that infers the correlation relationship among members of microbial communities using compositional data obtained from high-throughput sequencing techniques for 16S rRNA gene profiling. It uses a novel method called CCLasso based on least squares with penalty to infer the correlation network for latent variables of compositional data from metagenomic data. CCLasso outperforms existing methods in edge recovery for compositional data and compares well with other methods in estimating the correlation network of microbe species from the Human Microbiome Project.

Topic

Metagenomics;Statistics and probability;Ecology

Detail

  • Operation: Correlation

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU LESSER GENERAL PUBLIC LICENSE v3

  • Cost: Free

  • Version name: 2.0

  • Credit: The National Natural Science Foundation of China, the National Key Basic Research Project of China, Graduate School of Peking University, National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: dengmh@math.pku.edu.cn, Fang Huaying hyfang@pku.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • CCLasso: correlation inference for compositional data through Lasso.
  • Fang H, et al. CCLasso: correlation inference for compositional data through Lasso. CCLasso: correlation inference for compositional data through Lasso. 2015; 31:3172-80. doi: 10.1093/bioinformatics/btv349
  • https://doi.org/10.1093/bioinformatics/btv349
  • PMID: 26048598
  • PMC: PMC4693003

Download and documentation

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