IHWpaper

DOI:10.18129/B9.bioc.IHWpaper

Reproduce figures in IHW paper

Bioconductor version: Release (3.13)

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

Installation

To install this package, start R (version "4.1") and enter:

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

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

Documentation

查看文档的版本包age 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	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	bob 体育平台下载 ,bob 体育平台下载 ,bob 体育平台下载 ,bob 体育平台下载
Version	1.20.0
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
LinkingTo	Rcpp
Suggests	testthat,RColorBrewer,wesanderson,scales,gridExtra,BiocStyle,knitr,rmarkdown,airway,locfdr,tidyr,ggbio,latex2exp
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	IHWpaper_1.20.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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	//www.anjoumacpherson.com/packages/IHWpaper/
Package Downloads Report	Download Stats