DOI: 10.18129/B9.bioc.IHWpaper    

Reproduce figures in IHW paper

Bioconductor version: Release (3.6)

This package conveniently wraps all functions needed to reproduce the figures in the IHW preprint, available on biorXiv under http://biorxiv.org/content/early/2016/03/30/034330. 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")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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


biocViews ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch
Version 1.6.0
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, pasilla, DESeq, locfdr, tidyr
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_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/IHWpaper
Package Short Url http://bioconductor.org/packages/IHWpaper/
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