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Correlation inference software tools | 16S ribosomal RNA sequencing data analysis

Direct analysis of microbial communities in the environment and human body has become more convenient and reliable owing to the advancements of high-throughput sequencing techniques for 16S rRNA gene profiling. Inferring the correlation relationship…
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SPIEC-EASI
Desktop
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MDSINE
Desktop

MDSINE Microbial Dynamical Systems INference Engine

A suite of algorithms for inferring dynamical systems models from microbiome…

A suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. MDSINE performs all analysis steps from reading data files through to…

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MInt
Desktop

MInt

A Poisson-multivariate normal hierarchical model to learn direct interactions…

A Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. MInt controls for confounding predictors at…

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gCoda
Desktop

gCoda

Allows to estimate the sparse structure of inverse covariance for latent normal…

Allows to estimate the sparse structure of inverse covariance for latent normal variables. gCoda addresses the high dimensionality of the microbiome data by using a penalized maximum likelihood…

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CCLasso
Desktop

CCLasso Correlation inference for Compositional data through Lasso

A method based on least squares with L1 penalty after log ratio transformation…

A method based on least squares with L1 penalty after log ratio transformation for raw compositional data to infer the correlations among microbes through a latent variable model. The simulation…

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SparCC
Desktop

SparCC

An approach that is capable of estimating correlation values from compositional…

An approach that is capable of estimating correlation values from compositional data. Additionally, SparCC contains a script for calculating the distance between samples using the JSD metric, its…

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mLDM
Desktop

mLDM metagenomic Lognormal-Dirichlet-Multinomial

Permits to discover associations among microbes and between microbes and their…

Permits to discover associations among microbes and between microbes and their environmental factors. mLDM is based on a hierarchical Bayesian model with sparsity constraints. It is able to consider…

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LOL
Desktop

LOL Lots Of Lasso

Optimizes various methods for Lasso inference with matrix wrapper. LOL offers…

Optimizes various methods for Lasso inference with matrix wrapper. LOL offers functions for breast cancer data set of genome-wide copy number merged data and expression of some important genes, to…

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FALCON
Desktop

FALCON

Identifies the viral and bacterial genomes that have similarity with a…

Identifies the viral and bacterial genomes that have similarity with a sequenced human genome. FALCON employs the relative algorithmic entropy method that is based on model-freezing and exclusive…

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