IHWpaper
Reproduce figures in IHW paper
Bioconductor version: Release (3.17)
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("IHWpaper")):
Installation
To install this package, start R (version "4.3") 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 |
Details
| biocViews | ExperimentData, ExpressionData, RNASeqData, ReproducibleResearch |
| Version | 1.28.0 |
| 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 |
| Linking To | Rcpp |
| Suggests | testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IHWpaper_1.28.0.tar.gz |
| Windows Binary | |
| 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/ |
| Package Downloads Report | Download Stats |