SPsimSeq - Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

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geneexpressionrnaseqsinglecellsequencingdnaseq

7.24 score 10 stars 1 dependents 36 scripts 326 downloads

RCM - Fit row-column association models with the negative binomial distribution for the microbiome

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

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metagenomicsdimensionreductionmicrobiomevisualizationordinationphyloseqrcm

7.09 score 16 stars 17 scripts 348 downloads

pim - Fit Probabilistic Index Models

Fit a probabilistic index model as described in Thas et al, 2012: <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the modeling function has changed in this new version. The old version is still available at R-Forge.

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modellingstatistics

5.34 score 11 stars 40 scripts 172 downloads

xnet - Two-Step Kernel Ridge Regression for Network Predictions

Fit a two-step kernel ridge regression model for predicting edges in networks, and carry out cross-validation using shortcuts for swift and accurate performance assessment (Stock et al, 2018 <doi:10.1093/bib/bby095> ).

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5.30 score 11 stars 12 scripts 179 downloads

reconsi - Resampling Collapsed Null Distributions for Simultaneous Inference

Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

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metagenomicsmicrobiomemultiplecomparisonflowcytometry

4.60 score 2 stars 2 scripts 302 downloads

combi - Compositional omics model based visual integration

This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.

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metagenomicsdimensionreductionmicrobiomevisualizationmetabolomics

4.56 score 1 stars 12 scripts 357 downloads