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This is the development version of IHWpaper; for the stable release version, see IHWpaper.

Reproduce figures in IHW paper

Bioconductor version: Development (3.20)

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper ( and the data analysis in, cf. the arXiv preprint ( Thus it is a companion package to the Bioconductor IHW package.

Author: Nikos Ignatiadis [aut, cre]

Maintainer: Nikos Ignatiadis <nikos.ignatiadis01 at>

Citation (from within R, enter citation("IHWpaper")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

NMeth paper: Explaining tdr HTML R Script
NMeth paper: IHW-Bonferroni simulations HTML R Script
NMeth paper: Real data examples HTML R Script
NMeth paper: Simulation Figures HTML R Script
NMeth paper: Stratified Histograms HTML R Script
Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli HTML R Script
Various: BH explanation / visualization HTML R Script
Various: Grenander Estimator as applied to IHW (vs ECDF) HTML R Script
Various: Real data examples: 1-fold weight function HTML R Script
Various: tdr and pvalue rejection regions HTML R Script
Various: Weights vs Independent Filtering HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version 1.33.0
License Artistic-2.0
Depends R (>= 3.3), IHW
Imports Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
System Requirements
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Suggests testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
Linking To Rcpp
Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IHWpaper_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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