• Phyloseq

  • Referenced in 8 articles [sw13730]
  • Reproducible Interactive Analysis and Graphics of Microbiome Census Data. Background: The analysis of microbial communities ... with limited support for high throughput microbiome census data...
  • PhyloScan

  • Referenced in 3 articles [sw34212]
  • Dirichlet-tree multinomial model for microbiome data. In this paper, we introduce the phylogenetic scan ... PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial ... model. DTM models the microbiome data through a cascade of independent local...
  • miLineage

  • Referenced in 1 article [sw34213]
  • taxonomic tree. Motivation: Association analysis of microbiome composition with disease-related outcomes provides invaluable knowledge ... disease mechanisms. Proper analysis of sparse compositional microbiome data is challenging. Existing methods rely ... with the covariates. Unlike existing methods for microbiome association analysis, our framework does not make ... distributional assumptions on the microbiome data; it allows for the adjustment of confounding variables...
  • microbiome

  • Referenced in 1 article [sw39388]
  • Bioconductor/R package microbiome: Microbiome Analytics. Utilities for microbiome analysis...
  • MicrobiomeAnalyst

  • Referenced in 1 article [sw26776]
  • comprehensive statistical, visual and meta-analysis of microbiome data. The widespread application of next-generation ... sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents ... datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational ... analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker...
  • ZIBBSeqDiscovery

  • Referenced in 1 article [sw41968]
  • ZIBBSeqDiscovery: Zero-Inflated Beta-Binomial Modeling of Microbiome Count Data. Microbiome count data (Operational Taxonomic ... association between the composition of the microbiome counts and the interested covariates...
  • MetamicrobiomeR

  • Referenced in 2 articles [sw26777]
  • MetamicrobiomeR: An R package for analysis of microbiome relative abundance data using zero-inflated beta...
  • CCLasso

  • Referenced in 2 articles [sw34287]
  • network of microbe species from the Human Microbiome Project. Availability and implementation: CCLasso is open...
  • MDSINE

  • Referenced in 1 article [sw26775]
  • MDSINE: Microbial dynamical systems inference engine for microbiome time-series analyses- Predicting dynamics of host ... algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors...
  • miProfile

  • Referenced in 1 article [sw34256]
  • based method that tests the association of microbiome composition with any covariates of interest. PERMANOVA ... approach by reanalyzing several real microbiome datasets. Availability and Implementation: miProfile software is freely available...
  • microViz

  • Referenced in 1 article [sw39387]
  • microViz: an R package for microbiome data visualization and statistics. R package for microbiome data...
  • HMP

  • Referenced in 1 article [sw26778]
  • power and sample size calculations for human microbiome experiments...
  • HMPTrees

  • Referenced in 1 article [sw26779]
  • Based Taxonomic Trees from Human Microbiome Data. Tools to model, compare, and visualize populations...
  • CARlasso

  • Referenced in 1 article [sw39712]
  • estimation of sparse microbial networks with predictors. Microbiome data analyses require statistical tools that...
  • MetaLonDA

  • Referenced in 1 article [sw41967]
  • longitudinal studies (Metwally AA, et al., Microbiome, 2018
  • Cuba

  • Referenced in 77 articles [sw00173]
  • Cuba -- a library for multidimensional numerical integration. The...
  • mclust

  • Referenced in 309 articles [sw00563]
  • R package mclust: Normal Mixture Modeling for Model...
  • polymake

  • Referenced in 316 articles [sw00724]
  • polymake is open source software for research in...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...