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.

Last updated 24 days ago

geneexpressionrnaseqsinglecellsequencingdnaseq

7.13 score 10 stars 1 packages 28 scripts 403 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.

Last updated 24 days ago

metagenomicsdimensionreductionmicrobiomevisualizationordinationphyloseqrcm

6.90 score 16 stars 25 scripts 149 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.

Last updated 5 years ago

modellingstatistics

5.32 score 10 stars 42 scripts 167 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> ).

Last updated 3 years ago

5.30 score 11 stars 12 scripts 130 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.

Last updated 24 days ago

metagenomicsmicrobiomemultiplecomparisonflowcytometry

4.60 score 2 stars 2 scripts 130 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.

Last updated 24 days ago

metagenomicsdimensionreductionmicrobiomevisualizationmetabolomics

4.48 score 1 stars 7 scripts 186 downloads