IHWpaper
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IHWpaper.
Reproduce figures in IHW paper
Bioconductor version: 3.7
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("IHWpaper")):
Installation
To install this package, start R (version "3.5") 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")| 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 | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch |
| Version | 1.7.0 |
| 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 |
See More
| Suggests | testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr, tidyr |
| 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_1.7.0.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 | https://bioconductor.org/packages/IHWpaper/ |
| Package Downloads Report | Download Stats |