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.
Last updated 5 months ago
metagenomicsdimensionreductionmicrobiomevisualization
16 stars 3.31 score 89 dependenciesSPsimSeq - 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.
Last updated 5 months ago
geneexpressionrnaseqsinglecellsequencingdnaseq
10 stars 2.27 score 134 dependencies 1 dependentsxnet - 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> ).
Last updated 3 years ago
11 stars 1.58 score 0 dependenciespim - 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.
Last updated 5 years ago
modellingstatistics
9 stars 1.46 score 3 dependenciescombi - 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.
Last updated 5 months ago
metagenomicsdimensionreductionmicrobiomevisualizationmetabolomics
1 stars 1.00 score 94 dependenciesreconsi - 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.
Last updated 5 months ago
metagenomicsmicrobiomemultiplecomparisonflowcytometry
2 stars 0.71 score 82 dependencies