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IHWpaper

Reproduce figures in IHW paper


Bioconductor version: Release (3.18)

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.

Author: Nikos Ignatiadis [aut, cre]

Maintainer: Nikos Ignatiadis <nikos.ignatiadis01 at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IHWpaper")

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

Documentation

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

browseVignettes("IHWpaper")
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

Details

biocViews ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version 1.30.0
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
URL
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Suggests testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package IHWpaper_1.30.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/IHWpaper
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IHWpaper
Package Short Url https://bioconductor.org/packages/IHWpaper/
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