IHWpaper

Reproduce figures in IHW paper


Bioconductor version: Release (3.20)

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 "4.4") 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 1.34.0
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
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Package Archives

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

Source Package IHWpaper_1.34.0.tar.gz
Windows Binary (x86_64)
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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