IHWpaper

DOI: 10.18129/B9.bioc.IHWpaper    

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

Reproduce figures in IHW paper

Bioconductor version: Development (3.8)

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available under 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 and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("IHWpaper", version = "devel")

Documentation

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

browseVignettes("IHWpaper")

 

HTML R Script 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 Stats paper: IHW-censoring & Storey simulations
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
PDF   Reference Manual

Details

biocViews ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version 1.9.4
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
LinkingTo Rcpp
Suggests testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package IHWpaper_1.9.4.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/IHWpaper/
Package Downloads Report Download Stats

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