CenterForStatistics-UGent/PIMseq-paper

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CenterForStatistics-UGent/PIMseq-paper

CenterForStatistics-UGent

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This repository contains codes and materials used in the PIMseq paper.

RCM

A model-based visualization method for microbiome data

SPsimSeq

Semi-parametric simulation of bulk and single cell RNA-seq data

xnet

xnet: a package for supervised network prediction

pim

R package for probabilistic index models

digipcr

digital PCR processing tools in R

unifiedWMWqPCR

Bioconductor package of unified Wilcoxon-Mann-Whitney test for qPCR

reconsi

Resample collapsed null distributions for simultaneous inference under dependence

Additional-File-6

Additional File 6

PIMseq

repository for the package PIMseq

NTCPmodels

Package implementing NTCP models

dPowerCalcR

Power calculations for digital PCR

smooth2

Additional Material for the book Smooth Tests of Goodness of Fit Using R

combi

Explorative integration of genomics data through multiplots

UCNR

Simulation code, case studies and tutorials for the Unified Censored Normal Regression model for qPCR analysis.

EBayesH

The R package EBayesH

mountainr

Bringing R and alpine to Docker

AppDGE

Shiny application to evaluate the performance of several differential gene expression tools for RNA-seq data.

Additional-File-2

This github repository includes R software codes used for a study on the evaluation of 14 differential gene expression methods for RNA-sequencing data (particularly for mRNA and lncRNA). The study has three main modules: (1) comparing selected normalization methods, (2) concordance analysis of 14 DGE analysis tools using 6 publicly accessible real RNA-seq data, and (3) non-parametric simulation study to evaluate tools with respect to false discovery rate and sensitivity.