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
7.17 score 10 stars 1 dependents 31 scripts 430 downloadspim - 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
5.59 score 11 stars 48 scripts 1.5k downloadsxnet - 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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5.36 score 11 stars 14 scripts 273 downloadsunifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.
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differentialexpressiongeneexpressionmicrotitreplateassaymultiplecomparisonqualitycontrolsoftwarevisualizationqpcr
4.00 score 1 scripts 514 downloads