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

PIMseq

repository for the package PIMseq

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

smooth2

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

UCNR

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

NTCPmodels

Package implementing NTCP models

dPowerCalcR

Power calculations for digital PCR

combi

Explorative integration of genomics data through multiplots

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.