metagenomeSeq

metagenomeSeq is an R tool to specify differentially abundant Operational Taxonomic Units (OTUs) and species features in high-throughput microbial marker-gene survey samples. The metagenomeSeq algorithm handles the normalization effects and under-sampling and includes testing of feature correlations.

Topic

Metagenomics;Sequencing

Detail

  • Operation: Sequence visualisation;Statistical calculation

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: The Artistic License 2.0

  • Cost: Free

  • Version name: 1.38.0

  • Credit: US National Science Foundation Graduate Research Fellowship, the Bill and Melinda Gates Foundation, the US National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: jpaulson@jimmy.harvard.edu

  • Collection: -

  • Maturity: Stable

Publications

  • Differential abundance analysis for microbial marker-gene surveys.
  • Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013 Dec;10(12):1200-2. doi: 10.1038/nmeth.2658. Epub 2013 Sep 29. PMID: 24076764; PMCID: PMC4010126.
  • https://doi.org/10.1038/nmeth.2658
  • PMID: 24076764
  • PMC: PMC4010126
  • Longitudinal differential abundance analysis of microbial marker-gene surveys using smoothing splines
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/https://doi.org/10.1101/099457
  • PMID: -
  • PMC: -

Download and documentation

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